Sam2matrix

This program determines for each read in the reference file if it has an entry in the provided sam files stating that it mapped. Afterwards a file is generated containing a row for each read which contains the read ID and the index of the mapped references.

Web Documentation for Sam2matrix

Input ports

1. Type: URI Object
   mapping [sam]
   File containing the mappings. [sam]
2. Type: URI Object
   reads [fq,fastq,fa,fasta,faa,ffn,fna,frn,embl,gbk,raw,sam]
   File containing the reads contained in the mapping file(s). [fq,fastq,fa,fasta,faa,ffn,fna,frn,embl,gbk,raw,sam]

Output ports

1. Type: URI Object
   out [tsv]
   Output file. [tsv]