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databio / pepatac

A modular, containerized pipeline for ATAC-seq data processing
http://pepatac.databio.org
BSD 2-Clause "Simplified" License
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is it possible to use aligned bam files as input ? #172

Closed pegahtak closed 3 years ago

pegahtak commented 3 years ago

Hello and thanks for great work. It's not an issue that I'm writing about but a question, so if it's irrelevant please let me know to delete or close this. I have about 250 aligned and deduplicated bam files that were aligned with bowtie2 and deduplicated using picard MarkDuplicates . I was wondering if I could use these bam files as input for pepatac ? Thank you

jpsmith5 commented 3 years ago

Hey @pegahtak, you would need to revert them (with Picard) to either an unaligned bam or generate fastq files from those.

For example: java -jar picard.jar RevertSam I=input.bam O=output_reverted.bam VALIDATION_STRINGENCY=LENIENT

Or: bedtools bamtofastq -i input.bam -fq output_r1.fq -fq2 output_r2.fq

See if that approach would work for you.

pegahtak commented 3 years ago

Thank you @jpsmith5