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TSS enrichment not reported when starting from BAMs

See original GitHub issue

Can you please adjust the pipeline to output TSS enrichment when the starting files are BAMs as opposed to FASTQ files? I’ve attached the config files and QC reports from two test runs: (1) starting from FASTQs; (2) starting from the filtered BAMs from (1). Both config files have atac.enable_tss_enrich set to true, but TSS scores are only reported in (1).

OS/Platform and dependencies

  • OS or Platform: SCG
  • Caper version 0.4.1

Issue Analytics

  • State:closed
  • Created 4 years ago
  • Comments:27 (5 by maintainers)

github_iconTop GitHub Comments

leepc12commented, Oct 28, 2019

We will have a user-defined read length array atac.read_len in the next release so that users can get TSS enrichment plot even when starting from BAMs.

nicolergcommented, Oct 28, 2019

@AbeerMM if it’s helpful, I copied the ENCODE python code to have a standalone script. I had to add os.environ['QT_QPA_PLATFORM']='offscreen' option to prevent some errors. You also need to point to the genome chromosome sizes. That was easy for me because I am using a custom genome database. Not sure what that looks like for pre-built genome databases. Otherwise, it works if I specify the read length as an integer.

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