StaticSection Parsing

Interaction pairs are parsed from the bam files using pairtools version 0.2.2. Filtering consists of several commands:

• pairtools parse
• Produces a pairsam file from an input bam file.
• The pairsam file is a pairs file, listing one read pair per line, with additional columns to track the sam-file lines, and a pairtools read classification.
• These classifications include information on whether the read aligned to 0, 1, or multiple places in the genome and whether it aligned end-to-end or if it was clipped.
• This tool also upper-triangularizes the reads, i.e. if the coordinate of second read is higher than the first, the reads are flipped.

• For more details, see the pairtools documentation.

• pairtools sort

• Produces a sorted pairsam file from an input pairsam file.

• Note that the flipping order and sort order of chromosomes is not identical. See the docs for more details.

• pairtools dedup --mark-dups

• (equivalent to pairtools markasdup)
• Identify duplicate alignments.

• Arbitrarily designate the duplicate status among the two duplicate alignments.

• pairtools select

• Remove duplicates, multi-mapped reads, and reads non-uniquely mapped at the 5' end.

Source files (v1.1.1_dcic_4):

• Workflow: https://data.4dnucleome.org/workflows/4DNWFMRGIPB1/
• CWL: https://github.com/4dn-dcic/iMARGI-Docker/blob/v1.1.1_dcic_4/src/cwl/imargi-processing-bam.cwl