BowtieToBedFormat.jar from Vancouver Short Read Analysis Package

[DrD2009]

Hello everyone,

I've been having problems using the BowtieToBedFormat tool that comes with the Vancouver Short Read Analysis Package. I have bowtie files in the default output and when I go to process them with the conversion tool it produces the output files:

Histogram.txt
log file
unpaired.tsv.gz
_simple_paired_samechr.tsv.gz
_simple_paired_spanchr.tsv.gz
_forked_paired.tsv.gz
_complex_paired.tsv.gz

Great right? Well, when I unzip the files they contain nothing or txt files that are blank.

Any suggestions? All I want to do is create a GFF or 3-column BED file from the bowtie output.


Thanks in advance,
Brandon

[frozenlyse]

you can use awk to turn a bowtie text output file into a 3 column bed file

awk -v bp=36 '{print $3"\t"$4"\t"($4+bp)}' infile.map > outfile.bed

set bp to however long your reads are, in this case 36bp
cheers

[DrD2009]

:O It works!! Haha.

I had to learn what awk was, but after that I installed it on my Debian box and it worked perfectly.

Is there a way for it to work for sequence length ranges? I do have a couple bowtie files where all of the sequence lengths are 17, but there are a few where the lengths range 15-26bps, is there a setting for that using awk?

Thank you so much.