This program will transpose data so that it is oriented by locus, instead of by sample. In additon, if paired-ends are available, the program will pull in the set of paired reads that are associate with each single-end locus that was assembled de novo.

Program Options

tsv2bam -P stacks_dir -M popmap [-R paired_reads_dir] tsv2bam -P stacks_dir -s sample [-s sample ...] [-R paired_reads_dir]

Example Usage

  1. Processing single-end data, de novo.

    Your Stacks directory should look similar to this, where the tags/snps/alleles/matches files were produced by the core pipeline (ustacks/cstacks/sstacks):

    % ls stacks/ sample_1020.alleles.tsv.gz sample_1069.alleles.tsv.gz sample_1086.alleles.tsv.gz sample_1095.alleles.tsv.gz sample_1020.matches.tsv.gz sample_1069.matches.tsv.gz sample_1086.matches.tsv.gz sample_1095.matches.tsv.gz sample_1020.snps.tsv.gz sample_1069.snps.tsv.gz sample_1086.snps.tsv.gz sample_1095.snps.tsv.gz sample_1020.tags.tsv.gz sample_1069.tags.tsv.gz sample_1086.tags.tsv.gz sample_1095.tags.tsv.gz

    % tsv2bam -P ./stacks/ -M ./popmap -t 8

  2. Processing paired-end data, de novo.

    Your Stacks directory should look the same as above, but we expect to find the paired-end reads files in the samples directory:

    % ls samples/ sample_1020.1.fq.gz sample_1069.1.fq.gz sample_1086.1.fq.gz sample_1095.1.fq.gz sample_1020.1.rem.fq.gz sample_1069.1.rem.fq.gz sample_1086.1.rem.fq.gz sample_1095.1.rem.fq.gz sample_1020.2.fq.gz sample_1069.2.fq.gz sample_1086.2.fq.gz sample_1095.2.fq.gz sample_1020.2.rem.fq.gz sample_1069.2.rem.fq.gz sample_1086.2.rem.fq.gz sample_1095.2.rem.fq.gz

    In this case, the sample_XXXX.1.fq.gz files were used by the core pipeline and now, tsv2bam will use the single-end read IDs from the assembled loci to find the corresponding paried-end reads in the sample_XXXX.2.fq files.

    % tsv2bam -P ./stacks/ -M ./popmap -R ./samples -t 8

Other Pipeline Programs

Raw Reads


Execution control