No counts from

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Yixuan Wan

May 16, 2023, 2:43:37 PMMay 16
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Hi Alex,

I am trying to generate files to quantify splice junctions with my RNA-seq data. 

I used values from column 7/8 as read counts. I compared the counts pulled from with outputs from another tool, I found contradicting results from them. While indicates that there is no read (i.e., count = 0) in particular loci, the other tool provides reads. I also used IGV and saw splice reads from both .bam and .bed files, which seems to indicate that the problem lies with the counts I pulled from

I guess I might do something wrong with my file. Do you have any suggestions?

Best Regards,

Alexander Dobin

May 16, 2023, 2:46:54 PMMay 16
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Hi Yixuan,

you would need to figure out which reads cross this junction, and then look at their alignments in the SAM file.
You can add jI and jM tags to the --outSAMattributes option to see which junctions the read overlaps.


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