[GenoMax]

Here is the error:

Microsoft Windows [Version 6.1.7601]
Copyright (c) 2009 Microsoft Corporation.  All rights reserved.

C:\Users\cmccabe>cd "C:\Users\cmccabe\Desktop\Ion_Torrent_ Software\bedtools-2.1
7.0"  (files here)

C:\Users\cmccabe\Desktop\Ion_Torrent_ Software\bedtools-2.17.0>[COLOR="Red"][SIZE="2"]bin\bedtools[/SIZE][/COLOR] bedToBam -i Ampli
cons.bed -g hg19_genome.txt > Amplicons.bam
'bedToBam' is not recognized as an internal or external command,
operable program or batch file.

Thanks.

I think you left out the executable program name "bedtools" when issuing the command. See the highlight in red.

[cmccabe]

$ 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

[GenoMax]

Should you not be running "bedToBam" if you are generating a BAM file?

[cmccabe]

What 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.

[GenoMax]

What 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.

In post #17 you had "bamToBed" listed instead of "bedToBam". Perhaps a typo or a wrong command?

[cmccabe]

bed2bam

I switched the command to bedToBam and got the same result. Maybe there is something wrong with the format of the BED file?

[GenoMax]

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)?

[cmccabe]

bed2bam

I am using the Cygwin Terminal to run the command. Thank you.

[GenoMax]

Can you try the following in cygwin terminal?

$ dos2unix Amplicons.bed
$ dos2unix hg19_genome.txt

This should reformat the files to unix file format.

Try running your bedToBam command again.

[cmccabe]

bed2bam

The file is is still 0kb, should I re-install cygwi and re-compile bedtools?

[Heisman]

Is your bed file tab-delimited? The two lines you posted don't appear to be although tabs may have been lost by copying/pasting.

[cmccabe]

bed2bam

Yes, the format of the BED is Tab-deliminated.

[GenoMax]

Once I explicitly changed the format in the example you pasted I was able to create the bam file.

What about your hg19_genome file?

[cmccabe]

bed2bam

The hg19_genome is also tab-deliminated.

[cmccabe]

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.