DE-kupl joinCounts is part of the DE-kupl package, and join multiple k-mer abundance files into a single matrix.
joinCounts input files must be tabulated files (possibly gziped) with the k-mer in the first column and the abundance in the second column. The input files must be sorted lexicographically by k-mer, and the files are to expected to containe a header line.
- Clone this repository :
git clone https://github.com/Transipedia/dekupl-joinCounts.git - Compile joinCounts :
make - Place the joinCounts binary somewhere acessible in your
$PATH
Counting and sorting 32-mer with Jellyfish
jellyfish count -m 32 -s 10000 -o sample.jf <(zcat sample.fastq.gz)
jellyfish dump -c sample.jf | sort -k 1 > counts.tsv
Consider using the sort command with -S {resources.ram}G and --parallel {threads} parameters to speed-up the sorting for large k-mer libraries.
Join counts from multiple libraries with joinCounts
joinCounts counts1.tsv counts2.tsv > counts-matrix.tsv