ChIP-seq TagPileup Data Cutoff and Full Fragment issue

[owlang]

In testing out ChIP-seq analysis with ENCODE data, we found a couple of issues possibly relating to the nature of the longer insert sizes of the ChIP-seq data.

Pileups of both 5prime and full-fragment settings result in the appearance of missing data:

Data accessions: ENCFF865UPM and ENCFF014UUB

I suspect the padding window set when TagPileup retrieves SamRecords from the BAM file is not large enough for the 5' end issue. Cannot comment yet on what is causing the full fragment issue and will need to test for differences with known working datasets

[owlang]

Fragment issue: Dataset was single-end 🙄

[owlang]

BED reference file was irregularly sized from the ENCODE liftOver to hg38 🙄

Not a bug. Be sure to add these warnings for single-end/ENCODE analysis in documentation. Closing ticket.