Originally posted by cmccabe
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$ cd /cygdrive/c/Users/cmccabe/Desktop/Ion_Torrent_ Software/bedtools-2.17.0
$ bin/bamToBed -i Amplicons.bed -g hg19_genome.txt > Amplicons.bam
The command runs in perl however the input Amplicons.bed in 44kb and the output amplicons.bam is 0kb. That doesent seem right and below is a couple lines from the BED file. Thanks.
chr1 2160290 2160475 AMPL2688828352 . SKI
chr1 2160480 2160634 AMPL2688829530 . SKI
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Originally posted by cmccabe View PostWhat I am trying to do is to calculate predicted off-target reads based on a BED file?
One sugesstion was to use bedToBam (from bedtools) followed by Picard's CalculateHSMetrics
Thanks.
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Since you are trying to do this on windows there could be some issue with file formats etc. It would be tough to diagnose them through the forum.
Do you think you would be up to trying this through the cygwin terminal (instead of windows terminal)?Last edited by GenoMax; 07-10-2013, 06:29 AM.
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bed2Bam
I re-compiled in cygwin
did dos2unix Amplicons.bed
dos2unix hg19_genome.txt
both of those files are tab- deliminated
and the commands I used in Cygwin:
$ cd "/cygdrive/c/Users/cmccabe/Desktop/Ion_Torrent_ Software/bedtools-2.17.0"
$ bin/bamToBed -i Amplicons.bed -g hg19_genome.txt > Amplicons.bam
Amplicons.bed (went from 44kb to 43kb)
chr1 2160290 2160475 SKI . AMPL2688828352
chr1 2160480 2160634 SKI . AMPL2688829530
chr1 2160632 2160738 SKI . AMPL2688828058
hg19_genome.txt (1kb) - acc chromosomes and lenghths are in this file
chr1 249,250,621
chr2 243,199,373
Amplicons.bam is still 0kb and not working.
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