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- align_bwa_illumina.sh - full NGS alignment pipeline using BWA
- align_bowtie2_illumina.sh - full NGS alignment pipeline using Bowtie2
- run_macs2.sh - pipeline to run the MACS2 peak-calling program
- gtf_to_bed.pl - converts a GTF-format annotation file to a tab-delimited BED-format file.
All these scripts use another file of functions in the ../script/ directory, common_functions.sh. It contains all the functions in cbb_common_functions.sh, as well as functions to perform work for the pipeline scripts; for example, to perform a BWA alignment. While there are parts of cbb_common_functions.sh that are specific to the TACC or BRCF pod environment, you might find it useful for building your own scripts.
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