can not support big chromosome

[shenweima]

I can run this command successfully, bamCoverage -b reads.bam -o coverage.bw
but the result is not complete.
When the chromosome size larger than 536Mb, there is nothing in bw file.

[dpryan79]

The BigWig format itself doesn't support chromosomes longer than that. In the future I should have the underlying library throw an error in cases like this, so people aren't surprised.

…

On 09/17/2018 05:49 PM, shenweima wrote: I can run this command successfully, |bamCoverage -b reads.bam -o coverage.bw| but the result is not complete. When the chromosome size larger than 536Mb, there is nothing in bw file. <https://camo.githubusercontent.com/99452a20f98127452d9f48bfec72b17b064ed900/68747470733a2f2f77686561742d313235323038383437322e70696373682e6d7971636c6f75642e636f6d2f323031382d30392d31372d3135343530382e706e67> — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#761>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGGkGPJiMUdLaCGmDvWtQBfL3OLEOWQbks5ub8SegaJpZM4WsM0Y>.

-- Devon Ryan, PhD Bioinformatician / Data manager Bioinformatics Core Facility Max Planck Institute for Immunobiology and Epigenetics Email: dpryan79@gmail.com

[dpryan79]

I'm reopening this, the bigWig limit is actually ~4GB, which should more than suffice. There are issues with older BAM indexing formats only supporting up to 536MB, but newer versions of pysam should handle that. I'll look further into whether this is an issue with deepTools, pysam, pyBigWig, or IGV.

[dpryan79]

It looks like one just has to make a CSI index. That works with the wheat genome, which has the largest chromosomes I can find.