BlastTab.seqdepth_nomedian.pl
Estimates the sequencing depth of subject sequences. The values reported by this script may differ from those of BlastTab.seqdepth.pl, because this script uses the aligned length of the read while BlastTab.seqdepth.pl uses the aligned length of the subject sequence.
See source code, Artistic license 2.0.
§ References
Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.
§ Requirements
- Perl.
§ Usage
BlastTab.seqdepth_nomedian.pl cat in_file | [opts] in_file > out_file
§ Arguments
- Input file*
in_file
One or more Tabular BLAST files of reads vs genes (or contigs).- Script
task
- genes_or_ctgs.fna*
in_file
A FastA file containing the genes or the contigs (db).- genes_or_ctgs.cov*
out_file
A tab-delimited file with the following columns: (1) Subject ID. (2) Average sequencing depth. (3) Number of mapped reads. (4) Length of the subject sequence.