Comments (19)
Please try:
cut -f 3 SPRINT_identified_all.res > SPRINT_identified_all.res.col3
bedtools intersect -a SPRINT_identified_all.res.col3 -b wheat.bed -u
from sprint.
Please try:
cut -f 1,2,3 SPRINT_identified_all.res > SPRINT_identified_all.res.col3
bedtools intersect -a SPRINT_identified_all.res.col3 -b wheat.bed -u
If it doesn’t work, can you send me some lines of your files using Email?
Feng
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Have you tried to use the wheat.bed to annotated other files. Can you change it into a standard BED format file?
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BED file should be TAB delimited.
Demo:
1A 7058 7215 GENE ID STRAND
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Please try to use this bed:
cut -f 1,2,3,4,5,6 wheat.bed > wheat_col6.bed
bedtools intersect -a SPRINT_identified_all.res.col3 -b wheat_col6.bed -wa -wb > output.bed
from sprint.
Please see
Maybe you need to sort your two bed files
from sprint.
Can you try BEDOPS?
bedops --intersect a.bed b.bed > output.bed
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bedmap --echo res.bed gene.bed> mapped.bed
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yes
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wheat_col6.sorted.bed
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Please follow the instruction (https://bedops.readthedocs.io/en/latest/content/reference/statistics/bedmap.html) to adjust the "echo" parameter.
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-
You can write script to solve this problem.
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Or, you can use the "match" function in EXCEL: https://exceljet.net/excel-functions/excel-match-function
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The most important part of SPRINT is the clustering of duplet editing sites.
You can try to apply SPRINT to identify editing on 16s rRNA.
But I’m not sure about that whether there is “duplet editing sites” on 16s rRNA.
You can change the clustering parameters based on the help manual of SPRINT.
https://github.com/jumphone/SPRINT/blob/master/SPRINT_manual.pdf
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my question is " SPRINT can be worked on DNA sequence ?? " ???????
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SPRINT is designed for "detecting" editing sites, not "predicting".
If there are duplet DNA editing sites on DNA sequence, SPRINT can detect them.
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You can use this sequence as a reference and then apply SPRINT to your NGS data.
If you don't have NGS data, SPRINT cannot help you.
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Please see #7
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What kind of species did you analyzed?
You can download the repeat annotation file from: https://sourceforge.net/projects/sprintpy/files/dbRES/.
Feng
from sprint.
I'm not familiar with the repeat regions of plant.
Maybe you can use SPRINT without using repreat annotation file.
Feng
from sprint.
Related Issues (20)
- How to set the parameter -ss for non-strand-specific RNA-seq? Thank you. HOT 2
- Is the trimming first 6 bases step included in your pipeline? HOT 2
- Why the rate of A-to-G deteced by SPRINT is very low ? HOT 3
- Generated binary files not working HOT 6
- zz2sam.py hard-codes strandedness HOT 5
- how to calculate the no. of editing sites present in 3' UTRs and CDS and 5'TRS??? HOT 3
- Effect of editing sites on the condon changes HOT 3
- SPRINT installation Error HOT 7
- Differential RNA Editing HOT 3
- Error during run HOT 6
- Execution problem HOT 3
- No output after execution HOT 4
- import error HOT 3
- reverse strandedness -ss 1 or -ss 2 HOT 4
- No results in final result files HOT 2
- calculation time HOT 1
- What ref .fa file to use for sprint main after prepare? HOT 1
- Main command causing issue with getA2I.py HOT 8
- Some editing sites can not be identified but it has editing reads when viewing with IGV. HOT 3
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