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Published 20 hours ago • verified publisher icon kaizhang

Could we provide more parameters for exporting bigwig files?

Open beyondpie opened this issue 1 year ago • 5 comments

Hi Kai,

Is that possible we can provide more parameters to simulate the behavior of bamCovrage: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html

I think it might be not our goal to support all the parameters in bamCoverage, but is that possible to support smoothLength, extendReads? The two parameters are used often during our analysis and should be easy for SnapATAC2 to support them in Rust layer (I guess the function is implemented there)?

Thanks! Songpeng

beyondpie avatar Oct 21 '24 04:10 beyondpie

Sure. I will implement it.

kaizhang avatar Oct 21 '24 04:10 kaizhang

Thank you so much!

beyondpie avatar Oct 21 '24 05:10 beyondpie

I added smooth_length to export_coverage: de58d01f1b74cb536f608ea27610b646bff9e7ff. Note the meaning of this parameter is different from bamcoverage. Please read the docs. For extendReads, SnapATAC2 already extends the fragment reads.

kaizhang avatar Oct 23 '24 09:10 kaizhang

@beyondpie Please let me know if there are any issues when you have a chance to test the new feature!

kaizhang avatar Oct 24 '24 09:10 kaizhang

@beyondpie Thank you! I will give it a try later. (After I send the issue, I use bed2bam and then use bamCoverage directly)

beyondpie avatar Oct 24 '24 15:10 beyondpie