Zero counts for whole LY75

[cwtkiwi]

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]

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.

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On Mar 15, 2018 7:05 AM, "cwtkiwi" ***@***.***> 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 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#32>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACwu7P_b3CSc8LJYcWBAnchHfibs-6zgks5tekr9gaJpZM4Sr8u1> .

[cwtkiwi]

Thank you very much for your reply!