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hartleys / JunctionSeq

The JunctionSeq R package is a powerful tool for testing and visualizing differential usage of exons and splice junctions in next-generation, high-throughput RNA-Seq experiments.
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Zero counts for whole LY75 #32

Open cwtkiwi opened 6 years ago

cwtkiwi commented 6 years ago

Dear Mr. Hartley,

I run the junctionSeq on a cohort with 68 libraries and chose the use.multigene.aggregates=TRUE mode. Somehow in the result all bins in gene LY75 (ENSG00000223972+ENSG00000227232+ENSG00000243485) are zero. Would it possible to improve this? Could there be anything wrong with configuring this gene or annotating this gene some where? Since this is a very important gene for our study, your help would be highly appreciated!!!

Best, Wengtein

hartleys commented 6 years ago

Have you checked the bam files for coverage on this gene? You can open the raw BAM files in IGV. Try this for a few bam files, just to check. This will tell you if you have data for this gene, or if perhaps there is some other problem.

You can also extract the region using samtools and view the SAM lines directly.

On Mar 15, 2018 7:05 AM, "cwtkiwi" notifications@github.com wrote:

Dear Mr. Hartley,

I run the junctionSeq on a cohort with 68 libraries and chose the use.multigene.aggregates=TRUE mode. Somehow in the result all bins in gene LY75 (ENSG00000223972+ENSG00000227232+ENSG00000243485) are zero. Would it possible to improve this? Could there be anything wrong with configuring this gene or annotating this gene some where? Since this is a very important gene for our study, your help would be highly appreciated!!!

Best, Wengtein

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cwtkiwi commented 4 years ago

Thank you very much for your reply!