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deeptools / deepTools

Tools to process and analyze deep sequencing data.
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bamCoverage does not accept trancriptome mapped alignment files #1010

Open kaltinel opened 4 years ago

kaltinel commented 4 years ago

Hi,

I am using transcriptome mapped alignment files and I wanted to visualize them on IGV in bigwig format. However, as far as I understand, bamCoverage is not able to do this, but rather wants a genome mapped alignment files? (My bigwig files were empty -aka no coverage- on IGV).

I would be happy to learn more about this, it would be nice to use bamCoverage. Thanks!

LeilyR commented 4 years ago

I am afraid it is not bamCoverage but IGV. Did you really get empty bigwig files? (file size = 0) This should not have happened if you had mapped reads on transcripts. The reason you cannot see them on IGV though, is that you most probably use the reference genome for your data not a transcripts reference so non of the chromosome names match and you get empty track.

kaltinel commented 4 years ago

Thank you for your reply.

No, the bigwig files are not empty, they just show no coverage. I will try with the transcript genome file and see if it works.