Comments (1)
qqwang-berkeley
commented on August 12, 2024
Hi,
Depending on your organism. For drosophila, 20M should be enough. For humans, I would recommend >20-30M.
poly-A or ribodepletion are both fine. I have used JUM to analyze both libraries. Just note, for the ribodepeletion library the quality will vary based on the experimental execution, as the ribos may not be completely depleted from time to time. But you can tell right away from the mapping step, as the ones mapped to ribos will be multi-mapped and you should be able to check the ratio v.s. uniquely mapped.
Qingqing
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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
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- 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
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