wham_bam

Simple script to convert all fastq files in a directory into bam files

Brought to you by: rabadger

Last Update: 2016-07-06

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The script takes fastq files from sequence runs (or from bam files converted using bam2fastq) and aligns to a user-selected genome.

Additional options to only convert reads above a certain mapping score, removing duplicates and generating bed files (requires Bedtools set in path).

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2012-10-26

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