Multiple fasta to one fasta in galaxy

Question

[rus2dil]

I have something like this >Chr6 C >Chr6 A >Chr6 C >Chr6 A >Chr6 T >Chr6 C I need something like this >Chr6 CACATC Need to use galaxy

[BioApps]

Why is your fasta file(s) looking like this?

[rus2dil]

It is because after mapping with BWA, generated pile up, the converted to fasta, which resulted single fasta file with multiple sequences.

[Matt Shirley]

It looks like this answer: How To Generate A Consensus Sequence On The Galaxy Platform might be what you're looking for instead.

Answer 1

[venu]

Assuming your file is same as what you have shown here, following should work

perl -pe 's/\s\S\w{3}\d{1}\s//g' yourFile.fasta > outputFile.fasta

Answer 2

[Jennifer Hillman Jackson]

Hello,

Protocol #5 in this pub shows exactly how to manipulate MAF data in Galaxy. Filter with regex, convert formats, etc. It is open source and the examples are in a live tutorial with a video: http://usegalaxy.org/u/galaxyproject/p/using-galaxy-2012

Thanks, Jen, Galaxy team