Multiple fasta to one fasta in galaxy
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6.6 years ago
rus2dil ▴ 20
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
galaxy fasta convertion sequencing sequence • 1.4k views
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Why is your fasta file(s) looking like this?

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It is because after mapping with BWA, generated pile up, the converted to fasta, which resulted single fasta file with multiple sequences.
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It looks like this answer: A: How To Generate A Consensus Sequence On The Galaxy Platform might be what you're looking for instead.

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6.6 years ago
venu 6.9k

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

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6.6 years ago

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

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