off-target reads

[cmccabe]

Is there anyway to calculate predicted off-target reads based on a BED file? Thanks.

[Heisman]

Would bedToBam (from bedtools) followed by Picard's CalculateHSMetrics work?

[cmccabe]

bed2bam

I do not seem to have a bed2bam.sh in bedtools 2.17.0. Can someone plese provide this file or a link? Thank you.

[Heisman]

Maybe try to re-download bedtools 2.17? It should come with it. What do you see in the bin folder that comes with it (it should be there)?

[cmccabe]

bed2bam

I re-downloaded 2.17 and do not see a bin folder. I have:

data
docs
genomes
scripts
src
test

In the test folder there are .sh files but not for bed2bam

In the src folder there is a bed2bam.cpp.

The error that I get in cygwin is can not open perl script bed2bam:

perl bedToBam -i Amplicons.bed -g hg1g_genome.txt > Amplicons.bam

Thank you.

[GenoMax]

You need to compile the bedtools package. What you have downloaded is the source code.

[cmccabe]

bed2bam

where do I download the correct package for cygwin? Thanks.

[GenoMax]

where do I download the correct package for cygwin? Thanks.

You will have to compile the package yourself. Bedtools is not supplied in binary form for cygwin.

You may need to install "gcc-g++" compiler for cygwin along with the make utility, zlib, zlib-devel library. You also need to install python.

Run the "setup.exe" for cygwin and then select these packages when you get to the package install screen.

[cmccabe]

bed2bam

The bedtools package has been compiled for cygwin and the bin folder appears.

perl bedToBam -i Amplicons.bed -g hg19_genome.txt > Amplicons.bam
Can't open perl script "bedToBam": No such file or directory

bedToBam -i Amplicons.bed -g hg19_genome.txt > Amplicons.bam
-bash: bedToBam: command not found. I can not find the error. Thanks.

[GenoMax]

The bedtools package has been compiled for cygwin and the bin folder appears.

perl bedToBam -i Amplicons.bed -g hg19_genome.txt > Amplicons.bam
Can't open perl script "bedToBam": No such file or directory

bedToBam -i Amplicons.bed -g hg19_genome.txt > Amplicons.bam
-bash: bedToBam: command not found. I can not find the error. Thanks.

You now have a compiled application. You do not need perl to run it (this is a C program BTW).

Run it like this (replace "path_to" with the actual directory path). This assumes that you are in the directory where the Amplicons.bed/hg19_genome files are.

$ /path_to/bin/bedToBam -i Amplicons.bed -g hg19_genome.txt > Amplicons.bam

[cmccabe]

bed2bam

I get this error:
Microsoft Windows [Version 6.1.7601]
Copyright (c) 2009 Microsoft Corporation. All rights reserved.

C:\Users\cmccabe>cd "C:\Users\cmccabe\Desktop\bedtools-2.17.0" (both files are here)

C:\Users\cmccabe\Desktop\bedtools-2.17.0>\Desktop\bedtools-2.17.0/bin/bedToBam -
i Amplicons.bed -g hg19_genome.txt > Amplicons.bam
The system cannot find the path specified.

Thanks.

[Heisman]

I haven't used Cygwin but it is weird to me that you have both "/" and "\" in your paths. You can try typing "pwd" to see the full path to the directory you are in.

[cmccabe]

bed2bam

Cygwin was only used as a compiler:

I am using cmd and getting that error.

[Heisman]

Oh, right. Could you try changing the "/" to "\"? And make sure all of the files are in the bedtools-2.17.0 folder.

[cmccabe]

bed2bam

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>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.