"I know the prosecutor in this case, and she is a very tough cookie." --Matlock
Matlock is a set of tools designed to work with Hi-C data. Functions include bam filtering, conversion, and clustering.
git clone --recursive https://github.com/phasegenomics/matlock.git matlock ; cd matlock ; make
usage: matlock <command> [options]
commands:
- bam2 - converts alignments to several useful hi-c formats.
+ usage: matlock bam2 [binmat|lachesis|juicer|counts] input output
+ details:
The input file format is automatically determined [cram|bam|sam].
The output is written to the fineame provided, no extention.
- bamfilt - filter a hi-c bam.
+ usage: matlock bamfilt input.[cram|bam|sam] output.bam
- motif - count motifs.
+ usage: matlock motif input.fasta ATGC TGCA ...