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buenrostrolab / mitoblacklist Public

forked from caleblareau/mitoblacklist

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mitoblacklist

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hg19wrap.sh

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mitoblacklist

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hg19wrap.sh

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12 lines (9 loc) · 313 Bytes

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#!/bin/bash

REF_hg38="/data/aryee/pub/genomes/bowtie2_index_hg38/hg38"

REF_hg19="/data/aryee/pub/genomes/bowtie2_index/hg19"

REF_mm10="/data/aryee/pub/genomes/mm10/bt2/mm10"

REF_mm9="/data/aryee/pub/genomes/bowtie2_index_mm9/mm9"

REF=$REF_hg19

FQ="fastq/hg19_dat.fq.gz"

out="hg19"

sh runStuff.sh $REF $FQ $out

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