Comments (5)
qqwang-berkeley
commented on August 12, 2024
Hi,
Would you show me the commands (parameters) you used, how many input samples you have (under which condition) and the sequencing depth of the samples?
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huiWyuan
commented on August 12, 2024
Hi
Thank you for your reply. My commands are show below(all sample has 2 replicates)
bash /home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master/JUM_A.sh --Folder /home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master --JuncThreshold 5 --Condition1_fileNum_threshold 2 --Condition2_fileNum_threshold 2 --IRthreshold 5 --Readlength 76 --Thread 10 --Condition1SampleName c1_rep1,c1_rep2 --Condition2SampleName c2_rep1,c2_rep2
Rscript /home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master/R_script_JUM.R experiment_design.txt > outputFile.Rout 2> errorFile.Rout
bash /home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master/JUM_B.sh --Folder /home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master --Test pvalue --Cutoff 1 --TotalFileNum 4 --Condition1_fileNum_threshold 2 --Condition2_fileNum_threshold 2 --Condition1SampleName c1_rep1,c1_rep2 --Condition2SampleName c2_rep1,c2_rep2
bash /home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master/JUM_C.sh --Folder /home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master/ --Test pvalue --Cutoff 1 --TotalCondition1FileNum 2 --TotalCondition2FileNum 2 --REF /home/lfgu/bigdata/hitseq/xkcui/output_CLIP_seq_PE_STAR/GFFuniq/gmax.gp
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qqwang-berkeley
commented on August 12, 2024
OK. I need the following things from you:
1) When you run the JUM scripts, were there any error messages?
2) Can you send me the "ls -l -t" results in the folder *temp_JUM_A_run*
3) Can you send me the "ls -l -t" results in the folder *JUM_diff*
4) Can you send me the "ls -l -t" results in the folder
*temp_JUM_B_run_pvalue_1*
5) Can you send me the "ls -l -t" results in the folder *temp_JUM_C_run*
2)-4) is for me to check the temporary files generated during each JUM
scripts.
…On Thu, Aug 9, 2018 at 7:19 PM wanghuiyuan ***@***.***> wrote:
Hi
Thank you for your reply. My commands are show below(all sample has 2
replicates)
bash /home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master/JUM_A.sh --Folder
/home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master --JuncThreshold 5
--Condition1_fileNum_threshold 2 --Condition2_fileNum_threshold 2
--IRthreshold 5 --Readlength 76 --Thread 10 --Condition1SampleName
c1_rep1,c1_rep2 --Condition2SampleName c2_rep1,c2_rep2
Rscript /home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master/R_script_JUM.R
experiment_design.txt > outputFile.Rout 2> errorFile.Rout
bash /home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master/JUM_B.sh --Folder
/home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master --Test pvalue --Cutoff 1
--TotalFileNum 4 --Condition1_fileNum_threshold 2
--Condition2_fileNum_threshold 2 --Condition1SampleName c1_rep1,c1_rep2
--Condition2SampleName c2_rep1,c2_rep2
bash /home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master/JUM_C.sh --Folder
/home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master/ --Test pvalue --Cutoff 1
--TotalCondition1FileNum 2 --TotalCondition2FileNum 2 --REF
/home/lfgu/bigdata/hitseq/xkcui/output_CLIP_seq_PE_STAR/GFFuniq/gmax.gp
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huiWyuan
commented on August 12, 2024
Hi
Actually, there are no error messages when I run the JUM_A.sh in the first step. But all intersect_short_intron2 files are zero in temp_JUM_A_run. Is that normal？
-rw-rw-r-- 1 lfgu lfgu 0 Aug 9 23:50 c1_rep1Aligned.out_intersect_short_intron2.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c1_rep1Aligned.out_intersect_short_intron2_chr_coor.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c1_rep1Aligned.out_intersect_short_intron2_count_table
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c1_rep1Aligned.out_intersect_short_intron2_edited.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 9 23:50 c1_rep2Aligned.out_intersect_short_intron2.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c1_rep2Aligned.out_intersect_short_intron2_chr_coor.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c1_rep2Aligned.out_intersect_short_intron2_count_table
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c1_rep2Aligned.out_intersect_short_intron2_edited.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 9 23:52 c2_rep1Aligned.out_intersect_short_intron2.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c2_rep1Aligned.out_intersect_short_intron2_chr_coor.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c2_rep1Aligned.out_intersect_short_intron2_count_table
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c2_rep1Aligned.out_intersect_short_intron2_edited.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 9 23:48 c2_rep2Aligned.out_intersect_short_intron2.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c2_rep2Aligned.out_intersect_short_intron2_chr_coor.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c2_rep2Aligned.out_intersect_short_intron2_count_table
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c2_rep2Aligned.out_intersect_short_intron2_edited.txt
there are no error messages when I run the R_script_JUM.R In the second step. All files in JUM_diff are normal
-rw-rw-r-- 1 lfgu lfgu 9.8M Aug 10 02:06 AS_differential.txt
drwxrwxr-x 3 lfgu lfgu 8.0K Aug 10 02:56 FINAL_JUM_OUTPUT_pvalue_1
-rw-rw-r-- 1 lfgu lfgu 1.5M Aug 9 20:06 UNION_junc_coor_with_junction_ID_more_than_5_read_in_at_least_2_samples.txt
-rw-rw-r-- 1 lfgu lfgu 365M Aug 10 00:01 c1_rep1Aligned.out_coverage.bed
-rw-rw-r-- 1 lfgu lfgu 1.3M Aug 10 00:03 c1_rep1_combined_count.txt
-rw-rw-r-- 1 lfgu lfgu 358M Aug 10 00:01 c1_rep2Aligned.out_coverage.bed
-rw-rw-r-- 1 lfgu lfgu 1.3M Aug 10 00:03 c1_rep2_combined_count.txt
-rw-rw-r-- 1 lfgu lfgu 430M Aug 10 00:01 c2_rep1Aligned.out_coverage.bed
-rw-rw-r-- 1 lfgu lfgu 1.3M Aug 10 00:03 c2_rep1_combined_count.txt
-rw-rw-r-- 1 lfgu lfgu 402M Aug 9 23:59 c2_rep2Aligned.out_coverage.bed
-rw-rw-r-- 1 lfgu lfgu 1.3M Aug 10 00:03 c2_rep2_combined_count.txt
-rw-rw-r-- 1 lfgu lfgu 7.1M Aug 10 00:02 combined_AS_JUM.gff
-rw-rw-r-- 1 lfgu lfgu 1.9K Aug 10 02:03 errorFile.Rout
-rw-rw-r-- 1 lfgu lfgu 79 Aug 10 01:53 experiment_design.txt
-rw-rw-r-- 1 lfgu lfgu 843K Aug 9 20:06 more_than_5_profiled_total_AS_event_junction_first_processing_for_JUM_reference_building.txt
-rw-rw-r-- 1 lfgu lfgu 214 Aug 10 02:00 outputFile.Rout
drwxrwxr-x 4 lfgu lfgu 12K Aug 10 02:51 temp_JUM_B_run_pvalue_1
when I run the JUM_B.sh In the third step. some files in temp_JUM_B_run_pvalue_1 are abnormal
-rw-rw-r-- 1 lfgu lfgu 6.9M Aug 10 02:47 AS_differential_JUM_output.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51 AS_differential_JUM_output_total_MXE.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51 AS_differential_JUM_output_total_cassette_exon.txt
-rw-rw-r-- 1 lfgu lfgu 1.7M Aug 10 02:51 AS_differential_JUM_output_total_mixed.txt
-rw-rw-r-- 1 lfgu lfgu 9.8M Aug 10 02:47 AS_differential_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51 AS_differential_pvalue_1_A3SS_event_AS_structure_list.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51 AS_differential_pvalue_1_A5SS_event_AS_structure_list.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51 AS_differential_pvalue_1_MXE_AS_event_list.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51 AS_differential_pvalue_1_cassette_exon_AS_event_list.txt
-rw-rw-r-- 1 lfgu lfgu 20K Aug 10 02:50 AS_differential_pvalue_1_long_intron_retention_passing_filter_combined_list.txt
-rw-rw-r-- 1 lfgu lfgu 64K Aug 10 02:51 AS_differential_pvalue_1_mixed_AS_event_list.txt
-rw-rw-r-- 1 lfgu lfgu 190K Aug 10 02:47 AS_differential_pvalue_1_non_intron_retention_AS_structure_list.txt
-rw-rw-r-- 1 lfgu lfgu 20K Aug 10 02:50 AS_differential_pvalue_1_valid_long_intron_retention_list.txt
-rw-rw-r-- 1 lfgu lfgu 8.2K Aug 10 02:47 AS_differential_pvalue_1_valid_short_intron_retention_list.txt
-rw-rw-r-- 1 lfgu lfgu 20K Aug 10 02:50 AS_differential_total_long_intron_retention_passing_filter_combined_list.txt
-rw-rw-r-- 1 lfgu lfgu 20K Aug 10 02:50 AS_differential_total_valid_long_intron_retention_list.txt
-rw-rw-r-- 1 lfgu lfgu 8.2K Aug 10 02:47 AS_differential_total_valid_short_intron_retention_list.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 MXE_coordinate_sorted.bed
-rw-rw-r-- 1 lfgu lfgu 365M Aug 10 02:48 c1_rep1Aligned.out_coverage_sorted.bed
-rw-rw-r-- 1 lfgu lfgu 85M Aug 10 02:48 c1_rep1_coverage_temp_long_intron_overlap_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 85M Aug 10 02:49 c1_rep1_coverage_temp_long_intron_overlap_total.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c1_rep1_coverage_temp_total_MXE_intersect.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c1_rep1_coverage_temp_total_cassette_intersect.txt
-rw-rw-r-- 1 lfgu lfgu 82K Aug 10 02:49 c1_rep1_long_intron_retention_screening_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 82K Aug 10 02:50 c1_rep1_long_intron_retention_screening_total.txt
-rw-rw-r-- 1 lfgu lfgu 312M Aug 10 02:48 c1_rep1_temp_long_intron_retention_junction_coordinate_with_read_num_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 312M Aug 10 02:50 c1_rep1_temp_long_intron_retention_junction_coordinate_with_read_num_total.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c1_rep1_temp_total_MXE_coordinate_with_read_num_per_ID.txt
-rw-rw-r-- 1 lfgu lfgu 5 Aug 10 02:50 c1_rep1_temp_total_MXE_with_indicator.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c1_rep1_temp_total_cassette_coordinate_with_read_num_per_ID.txt
-rw-rw-r-- 1 lfgu lfgu 5 Aug 10 02:50 c1_rep1_temp_total_cassette_with_indicator.txt
-rw-rw-r-- 1 lfgu lfgu 18K Aug 10 02:49 c1_rep1_valid_long_intron_retention_event_list_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 18K Aug 10 02:50 c1_rep1_valid_long_intron_retention_event_list_total.txt
-rw-rw-r-- 1 lfgu lfgu 1 Aug 10 02:50 c1_rep1_valid_total_MXE_event_ID.txt
-rw-rw-r-- 1 lfgu lfgu 1 Aug 10 02:50 c1_rep1_valid_total_cassette_exon_event_ID.txt
-rw-rw-r-- 1 lfgu lfgu 358M Aug 10 02:48 c1_rep2Aligned.out_coverage_sorted.bed
-rw-rw-r-- 1 lfgu lfgu 82M Aug 10 02:48 c1_rep2_coverage_temp_long_intron_overlap_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 82M Aug 10 02:49 c1_rep2_coverage_temp_long_intron_overlap_total.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c1_rep2_coverage_temp_total_MXE_intersect.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c1_rep2_coverage_temp_total_cassette_intersect.txt
-rw-rw-r-- 1 lfgu lfgu 82K Aug 10 02:49 c1_rep2_long_intron_retention_screening_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 82K Aug 10 02:50 c1_rep2_long_intron_retention_screening_total.txt
-rw-rw-r-- 1 lfgu lfgu 312M Aug 10 02:48 c1_rep2_temp_long_intron_retention_junction_coordinate_with_read_num_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 312M Aug 10 02:49 c1_rep2_temp_long_intron_retention_junction_coordinate_with_read_num_total.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c1_rep2_temp_total_MXE_coordinate_with_read_num_per_ID.txt
-rw-rw-r-- 1 lfgu lfgu 5 Aug 10 02:50 c1_rep2_temp_total_MXE_with_indicator.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c1_rep2_temp_total_cassette_coordinate_with_read_num_per_ID.txt
-rw-rw-r-- 1 lfgu lfgu 5 Aug 10 02:50 c1_rep2_temp_total_cassette_with_indicator.txt
-rw-rw-r-- 1 lfgu lfgu 18K Aug 10 02:49 c1_rep2_valid_long_intron_retention_event_list_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 18K Aug 10 02:50 c1_rep2_valid_long_intron_retention_event_list_total.txt
-rw-rw-r-- 1 lfgu lfgu 1 Aug 10 02:50 c1_rep2_valid_total_MXE_event_ID.txt
-rw-rw-r-- 1 lfgu lfgu 1 Aug 10 02:50 c1_rep2_valid_total_cassette_exon_event_ID.txt
-rw-rw-r-- 1 lfgu lfgu 430M Aug 10 02:48 c2_rep1Aligned.out_coverage_sorted.bed
-rw-rw-r-- 1 lfgu lfgu 115M Aug 10 02:48 c2_rep1_coverage_temp_long_intron_overlap_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 115M Aug 10 02:49 c2_rep1_coverage_temp_long_intron_overlap_total.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c2_rep1_coverage_temp_total_MXE_intersect.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c2_rep1_coverage_temp_total_cassette_intersect.txt
-rw-rw-r-- 1 lfgu lfgu 82K Aug 10 02:49 c2_rep1_long_intron_retention_screening_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 82K Aug 10 02:50 c2_rep1_long_intron_retention_screening_total.txt
-rw-rw-r-- 1 lfgu lfgu 313M Aug 10 02:48 c2_rep1_temp_long_intron_retention_junction_coordinate_with_read_num_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 313M Aug 10 02:50 c2_rep1_temp_long_intron_retention_junction_coordinate_with_read_num_total.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c2_rep1_temp_total_MXE_coordinate_with_read_num_per_ID.txt
-rw-rw-r-- 1 lfgu lfgu 5 Aug 10 02:50 c2_rep1_temp_total_MXE_with_indicator.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c2_rep1_temp_total_cassette_coordinate_with_read_num_per_ID.txt
-rw-rw-r-- 1 lfgu lfgu 5 Aug 10 02:50 c2_rep1_temp_total_cassette_with_indicator.txt
-rw-rw-r-- 1 lfgu lfgu 20K Aug 10 02:49 c2_rep1_valid_long_intron_retention_event_list_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 20K Aug 10 02:50 c2_rep1_valid_long_intron_retention_event_list_total.txt
-rw-rw-r-- 1 lfgu lfgu 1 Aug 10 02:50 c2_rep1_valid_total_MXE_event_ID.txt
-rw-rw-r-- 1 lfgu lfgu 1 Aug 10 02:50 c2_rep1_valid_total_cassette_exon_event_ID.txt
-rw-rw-r-- 1 lfgu lfgu 402M Aug 10 02:48 c2_rep2Aligned.out_coverage_sorted.bed
-rw-rw-r-- 1 lfgu lfgu 103M Aug 10 02:48 c2_rep2_coverage_temp_long_intron_overlap_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 103M Aug 10 02:49 c2_rep2_coverage_temp_long_intron_overlap_total.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c2_rep2_coverage_temp_total_MXE_intersect.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c2_rep2_coverage_temp_total_cassette_intersect.txt
-rw-rw-r-- 1 lfgu lfgu 82K Aug 10 02:49 c2_rep2_long_intron_retention_screening_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 82K Aug 10 02:50 c2_rep2_long_intron_retention_screening_total.txt
-rw-rw-r-- 1 lfgu lfgu 313M Aug 10 02:48 c2_rep2_temp_long_intron_retention_junction_coordinate_with_read_num_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 313M Aug 10 02:49 c2_rep2_temp_long_intron_retention_junction_coordinate_with_read_num_total.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c2_rep2_temp_total_MXE_coordinate_with_read_num_per_ID.txt
-rw-rw-r-- 1 lfgu lfgu 5 Aug 10 02:50 c2_rep2_temp_total_MXE_with_indicator.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c2_rep2_temp_total_cassette_coordinate_with_read_num_per_ID.txt
-rw-rw-r-- 1 lfgu lfgu 5 Aug 10 02:50 c2_rep2_temp_total_cassette_with_indicator.txt
-rw-rw-r-- 1 lfgu lfgu 19K Aug 10 02:49 c2_rep2_valid_long_intron_retention_event_list_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 19K Aug 10 02:50 c2_rep2_valid_long_intron_retention_event_list_total.txt
-rw-rw-r-- 1 lfgu lfgu 1 Aug 10 02:50 c2_rep2_valid_total_MXE_event_ID.txt
-rw-rw-r-- 1 lfgu lfgu 1 Aug 10 02:50 c2_rep2_valid_total_cassette_exon_event_ID.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 cassette_exon_coordinate_sorted.bed
drwxrwxr-x 2 lfgu lfgu 4.0K Aug 10 02:50 con1_3
drwxrwxr-x 2 lfgu lfgu 4.0K Aug 10 02:50 con2_3
-rw-rw-r-- 1 lfgu lfgu 2.8M Aug 10 02:47 left_span_long_intron_AS_differential_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 2.8M Aug 10 02:47 left_span_long_intron_AS_differential_total.txt
-rw------- 1 lfgu lfgu 24K Aug 10 02:51 nohup.out
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 non_valid_cassette_exon_list.txt
-rw-rw-r-- 1 lfgu lfgu 1.5M Aug 10 02:50 reconstruct_splicing_pattern_input_1.txt
-rw-rw-r-- 1 lfgu lfgu 670K Aug 10 02:50 reconstruct_splicing_pattern_input_2.txt
-rw-rw-r-- 1 lfgu lfgu 2.8M Aug 10 02:47 right_span_long_intron_AS_differential_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 2.8M Aug 10 02:47 right_span_long_intron_AS_differential_total.txt
-rw-rw-r-- 1 lfgu lfgu 7.2K Aug 10 02:47 run.sh
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51 temp_MXE
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51 temp_cassette
-rw-rw-r-- 1 lfgu lfgu 1.5M Aug 10 02:51 temp_intron_retention
-rw-rw-r-- 1 lfgu lfgu 987K Aug 10 02:51 temp_intron_retention_consistant
-rw-rw-r-- 1 lfgu lfgu 2.9M Aug 10 02:47 temp_long_intron_retention_AS_differential_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 64K Aug 10 02:47 temp_long_intron_retention_AS_differential_pvalue_1_list.txt
-rw-rw-r-- 1 lfgu lfgu 2.9M Aug 10 02:47 temp_long_intron_retention_AS_differential_total.txt
-rw-rw-r-- 1 lfgu lfgu 64K Aug 10 02:47 temp_long_intron_retention_AS_differential_total_list.txt
-rw-rw-r-- 1 lfgu lfgu 171K Aug 10 02:47 temp_long_intron_retention_junction_coordinate_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 171K Aug 10 02:47 temp_long_intron_retention_junction_coordinate_pvalue_1_sorted.txt
-rw-rw-r-- 1 lfgu lfgu 171K Aug 10 02:47 temp_long_intron_retention_junction_coordinate_total.txt
-rw-rw-r-- 1 lfgu lfgu 171K Aug 10 02:47 temp_long_intron_retention_junction_coordinate_total_sorted.txt
-rw-rw-r-- 1 lfgu lfgu 1.7M Aug 10 02:51 temp_mixed
-rw-rw-r-- 1 lfgu lfgu 343K Aug 10 02:51 test_intron.txt
-rw-rw-r-- 1 lfgu lfgu 67K Aug 10 02:51 test_intron_delta_consistant_and_no_inner_junction_list.txt
-rw-rw-r-- 1 lfgu lfgu 84K Aug 10 02:51 test_intron_delta_consistant_list.txt
-rw-rw-r-- 1 lfgu lfgu 499 Aug 10 02:51 title
-rw-rw-r-- 1 lfgu lfgu 35K Aug 10 02:50 total_A3SS_event.txt
-rw-rw-r-- 1 lfgu lfgu 58K Aug 10 02:50 total_A5SS_event.txt
-rw-rw-r-- 1 lfgu lfgu 35K Aug 10 02:50 total_cassette_exon_event.txt
Thanks!
from jum.
qqwang-berkeley
commented on August 12, 2024
If all intersect_short_intron2 files are zero from JUM_A.sh that is fine.
It just means that there were no super short intron retention events in
your sample.
I can help you debug the JUM_B.sh step.
1) Could you dropbox or google drive share with me the JUM_diff folder
(without the temp_JUM_B_run_pvalue_1 and FINAL_JUM_OUTPUT_pvalue_1
subdirectories). Basically, I am going to run JUM_B.sh on my end on your
files and see why AS events other than IR were empty. You can share your
folder with my email at: [email protected].
2) Could you send the two files: errorFile.Rout and outputFile.Rout?
These will record detailed information about running the Rscript step.
It is probably not something serious. Just need some checking.
…On Thu, Aug 9, 2018 at 8:43 PM wanghuiyuan ***@***.***> wrote:
Hi
actually, there are no error messages when I run the JUM_A.sh in the first
step. But all intersect_short_intron2 files are zero in temp_JUM_A_run. Is
that normal？
-rw-rw-r-- 1 lfgu lfgu 0 Aug 9 23:50
c1_rep1Aligned.out_intersect_short_intron2.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01
c1_rep1Aligned.out_intersect_short_intron2_chr_coor.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01
c1_rep1Aligned.out_intersect_short_intron2_count_table
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01
c1_rep1Aligned.out_intersect_short_intron2_edited.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 9 23:50
c1_rep2Aligned.out_intersect_short_intron2.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01
c1_rep2Aligned.out_intersect_short_intron2_chr_coor.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01
c1_rep2Aligned.out_intersect_short_intron2_count_table
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01
c1_rep2Aligned.out_intersect_short_intron2_edited.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 9 23:52
c2_rep1Aligned.out_intersect_short_intron2.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01
c2_rep1Aligned.out_intersect_short_intron2_chr_coor.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01
c2_rep1Aligned.out_intersect_short_intron2_count_table
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01
c2_rep1Aligned.out_intersect_short_intron2_edited.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 9 23:48
c2_rep2Aligned.out_intersect_short_intron2.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01
c2_rep2Aligned.out_intersect_short_intron2_chr_coor.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01
c2_rep2Aligned.out_intersect_short_intron2_count_table
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01
c2_rep2Aligned.out_intersect_short_intron2_edited.txt
All files in *JUM_diff* are normal
-rw-rw-r-- 1 lfgu lfgu 9.8M Aug 10 02:06 AS_differential.txt
drwxrwxr-x 3 lfgu lfgu 8.0K Aug 10 02:56 FINAL_JUM_OUTPUT_pvalue_1
-rw-rw-r-- 1 lfgu lfgu 1.5M Aug 9 20:06
UNION_junc_coor_with_junction_ID_more_than_5_read_in_at_least_2_samples.txt
-rw-rw-r-- 1 lfgu lfgu 365M Aug 10 00:01 c1_rep1Aligned.out_coverage.bed
-rw-rw-r-- 1 lfgu lfgu 1.3M Aug 10 00:03 c1_rep1_combined_count.txt
-rw-rw-r-- 1 lfgu lfgu 358M Aug 10 00:01 c1_rep2Aligned.out_coverage.bed
-rw-rw-r-- 1 lfgu lfgu 1.3M Aug 10 00:03 c1_rep2_combined_count.txt
-rw-rw-r-- 1 lfgu lfgu 430M Aug 10 00:01 c2_rep1Aligned.out_coverage.bed
-rw-rw-r-- 1 lfgu lfgu 1.3M Aug 10 00:03 c2_rep1_combined_count.txt
-rw-rw-r-- 1 lfgu lfgu 402M Aug 9 23:59 c2_rep2Aligned.out_coverage.bed
-rw-rw-r-- 1 lfgu lfgu 1.3M Aug 10 00:03 c2_rep2_combined_count.txt
-rw-rw-r-- 1 lfgu lfgu 7.1M Aug 10 00:02 combined_AS_JUM.gff
-rw-rw-r-- 1 lfgu lfgu 1.9K Aug 10 02:03 errorFile.Rout
-rw-rw-r-- 1 lfgu lfgu 79 Aug 10 01:53 experiment_design.txt
-rw-rw-r-- 1 lfgu lfgu 843K Aug 9 20:06
more_than_5_profiled_total_AS_event_junction_first_processing_for_JUM_reference_building.txt
-rw-rw-r-- 1 lfgu lfgu 214 Aug 10 02:00 outputFile.Rout
drwxrwxr-x 4 lfgu lfgu 12K Aug 10 02:51 temp_JUM_B_run_pvalue_1
there are no error messages when I run the R_script_JUM.R In the second
step. All files in *JUM_diff* are normal
-rw-rw-r-- 1 lfgu lfgu 9.8M Aug 10 02:06 AS_differential.txt
drwxrwxr-x 3 lfgu lfgu 8.0K Aug 10 02:56 FINAL_JUM_OUTPUT_pvalue_1
-rw-rw-r-- 1 lfgu lfgu 1.5M Aug 9 20:06
UNION_junc_coor_with_junction_ID_more_than_5_read_in_at_least_2_samples.txt
-rw-rw-r-- 1 lfgu lfgu 365M Aug 10 00:01 c1_rep1Aligned.out_coverage.bed
-rw-rw-r-- 1 lfgu lfgu 1.3M Aug 10 00:03 c1_rep1_combined_count.txt
-rw-rw-r-- 1 lfgu lfgu 358M Aug 10 00:01 c1_rep2Aligned.out_coverage.bed
-rw-rw-r-- 1 lfgu lfgu 1.3M Aug 10 00:03 c1_rep2_combined_count.txt
-rw-rw-r-- 1 lfgu lfgu 430M Aug 10 00:01 c2_rep1Aligned.out_coverage.bed
-rw-rw-r-- 1 lfgu lfgu 1.3M Aug 10 00:03 c2_rep1_combined_count.txt
-rw-rw-r-- 1 lfgu lfgu 402M Aug 9 23:59 c2_rep2Aligned.out_coverage.bed
-rw-rw-r-- 1 lfgu lfgu 1.3M Aug 10 00:03 c2_rep2_combined_count.txt
-rw-rw-r-- 1 lfgu lfgu 7.1M Aug 10 00:02 combined_AS_JUM.gff
-rw-rw-r-- 1 lfgu lfgu 1.9K Aug 10 02:03 errorFile.Rout
-rw-rw-r-- 1 lfgu lfgu 79 Aug 10 01:53 experiment_design.txt
-rw-rw-r-- 1 lfgu lfgu 843K Aug 9 20:06
more_than_5_profiled_total_AS_event_junction_first_processing_for_JUM_reference_building.txt
-rw-rw-r-- 1 lfgu lfgu 214 Aug 10 02:00 outputFile.Rout
drwxrwxr-x 4 lfgu lfgu 12K Aug 10 02:51 temp_JUM_B_run_pvalue_1
when I run the JUM_B.sh In the third step. some files in
temp_JUM_B_run_pvalue_1 are abnormal
-rw-rw-r-- 1 lfgu lfgu 6.9M Aug 10 02:47 AS_differential_JUM_output.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51
AS_differential_JUM_output_total_MXE.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51
AS_differential_JUM_output_total_cassette_exon.txt
-rw-rw-r-- 1 lfgu lfgu 1.7M Aug 10 02:51
AS_differential_JUM_output_total_mixed.txt
-rw-rw-r-- 1 lfgu lfgu 9.8M Aug 10 02:47 AS_differential_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51
AS_differential_pvalue_1_A3SS_event_AS_structure_list.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51
AS_differential_pvalue_1_A5SS_event_AS_structure_list.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51
AS_differential_pvalue_1_MXE_AS_event_list.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51
AS_differential_pvalue_1_cassette_exon_AS_event_list.txt
-rw-rw-r-- 1 lfgu lfgu 20K Aug 10 02:50
AS_differential_pvalue_1_long_intron_retention_passing_filter_combined_list.txt
-rw-rw-r-- 1 lfgu lfgu 64K Aug 10 02:51
AS_differential_pvalue_1_mixed_AS_event_list.txt
-rw-rw-r-- 1 lfgu lfgu 190K Aug 10 02:47
AS_differential_pvalue_1_non_intron_retention_AS_structure_list.txt
-rw-rw-r-- 1 lfgu lfgu 20K Aug 10 02:50
AS_differential_pvalue_1_valid_long_intron_retention_list.txt
-rw-rw-r-- 1 lfgu lfgu 8.2K Aug 10 02:47
AS_differential_pvalue_1_valid_short_intron_retention_list.txt
-rw-rw-r-- 1 lfgu lfgu 20K Aug 10 02:50
AS_differential_total_long_intron_retention_passing_filter_combined_list.txt
-rw-rw-r-- 1 lfgu lfgu 20K Aug 10 02:50
AS_differential_total_valid_long_intron_retention_list.txt
-rw-rw-r-- 1 lfgu lfgu 8.2K Aug 10 02:47
AS_differential_total_valid_short_intron_retention_list.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 MXE_coordinate_sorted.bed
-rw-rw-r-- 1 lfgu lfgu 365M Aug 10 02:48
c1_rep1Aligned.out_coverage_sorted.bed
-rw-rw-r-- 1 lfgu lfgu 85M Aug 10 02:48
c1_rep1_coverage_temp_long_intron_overlap_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 85M Aug 10 02:49
c1_rep1_coverage_temp_long_intron_overlap_total.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50
c1_rep1_coverage_temp_total_MXE_intersect.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50
c1_rep1_coverage_temp_total_cassette_intersect.txt
-rw-rw-r-- 1 lfgu lfgu 82K Aug 10 02:49
c1_rep1_long_intron_retention_screening_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 82K Aug 10 02:50
c1_rep1_long_intron_retention_screening_total.txt
-rw-rw-r-- 1 lfgu lfgu 312M Aug 10 02:48
c1_rep1_temp_long_intron_retention_junction_coordinate_with_read_num_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 312M Aug 10 02:50
c1_rep1_temp_long_intron_retention_junction_coordinate_with_read_num_total.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50
c1_rep1_temp_total_MXE_coordinate_with_read_num_per_ID.txt
-rw-rw-r-- 1 lfgu lfgu 5 Aug 10 02:50
c1_rep1_temp_total_MXE_with_indicator.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50
c1_rep1_temp_total_cassette_coordinate_with_read_num_per_ID.txt
-rw-rw-r-- 1 lfgu lfgu 5 Aug 10 02:50
c1_rep1_temp_total_cassette_with_indicator.txt
-rw-rw-r-- 1 lfgu lfgu 18K Aug 10 02:49
c1_rep1_valid_long_intron_retention_event_list_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 18K Aug 10 02:50
c1_rep1_valid_long_intron_retention_event_list_total.txt
-rw-rw-r-- 1 lfgu lfgu 1 Aug 10 02:50 c1_rep1_valid_total_MXE_event_ID.txt
-rw-rw-r-- 1 lfgu lfgu 1 Aug 10 02:50
c1_rep1_valid_total_cassette_exon_event_ID.txt
-rw-rw-r-- 1 lfgu lfgu 358M Aug 10 02:48
c1_rep2Aligned.out_coverage_sorted.bed
-rw-rw-r-- 1 lfgu lfgu 82M Aug 10 02:48
c1_rep2_coverage_temp_long_intron_overlap_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 82M Aug 10 02:49
c1_rep2_coverage_temp_long_intron_overlap_total.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50
c1_rep2_coverage_temp_total_MXE_intersect.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50
c1_rep2_coverage_temp_total_cassette_intersect.txt
-rw-rw-r-- 1 lfgu lfgu 82K Aug 10 02:49
c1_rep2_long_intron_retention_screening_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 82K Aug 10 02:50
c1_rep2_long_intron_retention_screening_total.txt
-rw-rw-r-- 1 lfgu lfgu 312M Aug 10 02:48
c1_rep2_temp_long_intron_retention_junction_coordinate_with_read_num_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 312M Aug 10 02:49
c1_rep2_temp_long_intron_retention_junction_coordinate_with_read_num_total.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50
c1_rep2_temp_total_MXE_coordinate_with_read_num_per_ID.txt
-rw-rw-r-- 1 lfgu lfgu 5 Aug 10 02:50
c1_rep2_temp_total_MXE_with_indicator.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50
c1_rep2_temp_total_cassette_coordinate_with_read_num_per_ID.txt
-rw-rw-r-- 1 lfgu lfgu 5 Aug 10 02:50
c1_rep2_temp_total_cassette_with_indicator.txt
-rw-rw-r-- 1 lfgu lfgu 18K Aug 10 02:49
c1_rep2_valid_long_intron_retention_event_list_pvalue_1.txt
-rw-rw-r-- 1 lfgu lfgu 18K Aug 10 02:50
c1_rep2_valid_long_intron_retention_event_list_total.txt
-rw-rw-r-- 1 lfgu lfgu 1 Aug 10 02:50 c1_rep2_valid_total_MXE_event_ID.txt
-rw-rw-r-- 1 lfgu lfgu 1 Aug 10 02:50
c1_rep2_valid_total_cassette_exon_event_ID.txt
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Related Issues (20)
- The length of the RNA-seq reads is inconsistent
- Can JUM be run on a single bam file ( only one treatment bam or only one control bam) HOT 6
- PSI values per condition HOT 1
- error occurred when running JUM_B.sh HOT 1
- Recommendations for sequencing depth HOT 1
- JUM output Splicing events Visualization tools HOT 1
- Correcting for batch effects while running JUM HOT 1
- JUM (v2.0.2 and up) stops and get killed at a certain step HOT 6
- Error of Rscript at write.table step HOT 1
- filtering outputs from cutoff p-value=1 HOT 3
- perl errors while running JUM_B HOT 1
- Perl Error due to a sample not having AS on one contig HOT 2
- JUM a lot of error... but finish runnnig an output empty file. HOT 1
- _trash_out file should be empty! HOT 2
- Regarding delta-PSI value, control-treatment vs treatment-control HOT 1
- Regarding Error "NONE" after running JUM_C.sh HOT 1
- JUM_A: ERROR: ... not sorted lexicographically HOT 1
- Error when running JUM_A.sh
- JUM_2-3.sh missing in JUM_3.0.0
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