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view LINKYX_reformat_trinity_header.sh @ 20:ea52ef8d7f3a

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added perl dependency since galaxy A seems working and added samtools sort
author biomonika <biomonika@psu.edu>
date Thu, 11 Sep 2014 19:17:11 -0400
parents 695d28139f3e
children
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#!/bin/bash

results=$1 #reformatted fasta sequence written here
trinity_fasta=${2}

perl -pe 's/(>[\S]+).+/$1/' $trinity_fasta >$results
samtools faidx $results