How To Transform The Bowtie Tabular Output Into Blast Tabular Output
I have a perl program SUmirFold13.pl
The SUmirFold13.pl only accept the the blast results in the format tabular (-outformat 6) like this
# Query ID Subject ID % length mism gaps qstart qend sstart send evalue bitscore
2-16 contig213144 100.00 23 0 0 1 23 910 888 0.10 38.0
2-16 contig1892305 95.65 23 1 0 1 23 447 469 0.94 34.9
I have the bowtie result(below)
# Query ID length qstart-qend Subject ID Subject-length sstart-send evalue unknown bitscore direction
2-16 23 1..23 contig213144 1892 983..1005 1e-04 1.00 42.1 Plus / Minus
2-16 23 1..23 contig1892305 721 447..469 1e-04 1.00 42.1 Plus / Plus
I think if the SUmirFold13.pl accept the bowtie result,it's good.I don't know how to modify the program，I hope someone give some suggestion.Thank you
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What are the names of the columns in the botwie output? Or, could you produce bowtie output for the same query as in the blast example?
I have edit it.
There are columns in the format you want to use that do not exist in the other file (mismatches, gaps). Unless you have the query and subject sequences, and a pairwise alignment of the two, you can't simply transform that bowtie output into the blast one, I'm afraid.
Does the tool use those columns?
Are you referring to: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0040859 ? The code is available in the supplementary material S1 in a PDF file (about the most intelligent way to distribute the code xD). If your code is different, please use a little less intrusive/obstructive site to deposit it, e.g. pastebin or github.
This perl was Written by Stuart J. Lucas,and I get this from him,there is no problem about it.
not the most intelligent way, but at least they bothered with publishing the code at all, instead of referring to the mysterious "in house script" ;-)