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StevenWingett / HiCUP

Hi-C data processing pipeline
GNU Lesser General Public License v3.0
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what is the difference between hicup.bam and pair.bam? Why not all files will produce hicup.bam? #69

Closed xsq2022 closed 2 years ago

xsq2022 commented 2 years ago

what is the difference between hicup.bam and pair.bam? Why not all files will produce hicup.bam?

StevenWingett commented 2 years ago

Hi,

The pair.bam file contains the di-tag information after mapping and pairing. The hicup.bam files contain the di-tag information after mapping, pairing, filtering and de-duplicating (i.e. once HiCUP has finished running).

You should have generated a *.hicup.bam (or sam) file once HiCUP has finished running successfully. To retain intermediate SAM/BAM files, add the --keep option to your initial command.

(If you have a .pair.bam file but no .hicup.bam file, then HiCUP has not completed successfully. Re-running HiCUP with more reserved RAM may resolve this).

Regards, Steven

xsq2022 commented 2 years ago

   Very happy to receive your reply. Thank you very much.---- Replied Message ----FromSteven @.>Date09/14/2022 23:31 @.> @.**@.>SubjectRe: [StevenWingett/HiCUP] what is the difference between hicup.bam and pair.bam? Why not all files will produce hicup.bam? (Issue #69) Closed #69 as completed.

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