Mercurial > repos > yating-l > bamtobigwig
changeset 2:f7f035d9d48a draft default tip
planemo upload commit 250051c3d660df43da92c76913552767ce142a45-dirty
author | yating-l |
---|---|
date | Tue, 30 May 2017 18:01:45 -0400 |
parents | 87341e6002eb |
children | |
files | bam_to_bigwig.xml |
diffstat | 1 files changed, 3 insertions(+), 1 deletions(-) [+] |
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--- a/bam_to_bigwig.xml Tue Feb 07 17:09:08 2017 -0500 +++ b/bam_to_bigwig.xml Tue May 30 18:01:45 2017 -0400 @@ -9,7 +9,9 @@ <command><![CDATA[ faToTwoBit $input_reference_fasta two_bit.2bit; twoBitInfo two_bit.2bit stdout | sort -k2nr > chrom.sizes; - bedtools genomecov -bg -split -ibam $input_bam -g chrom.sizes > temp.bg; + bedtools genomecov -bg -split -ibam $input_bam -g chrom.sizes + | LC_COLLATE=C sort -k1,1 -k2,2n + > temp.bg && bedGraphToBigWig temp.bg chrom.sizes $output_bigwig; ]]></command> <inputs>