[Heisman]

I'm really at a loss as to what's going on. Could you cd into the "/cygdrive/c/Users/cmccabe/Desktop/Ion_Torrent_ Software/bedtools-2.17.0" directory, type "ls -l", take a screen shot, and attach it?

[Heisman]

Also for fun do "head -3 Amplicons.bed | od -c" and "head -3 hg19_genome.txt | od -c" and copy and paste the output here.

[GenoMax]

I concur. Everything looks ok and should work. Let us see what the output is for the commands Heisman asked for.

[cmccabe]

bed2Bam

The results of the 3 commands:
cmccabe@DTV-L2231M5J ~
$ cd "/cygdrive/c/Users/cmccabe/Desktop/Ion_Torrent_ Software/bedtools-2.17.0"

cmccabe@DTV-L2231M5J /cygdrive/c/Users/cmccabe/Desktop/Ion_Torrent_ Software/bedtools-2.17.0
$ ls -l
total 177
-rwx------+ 1 cmccabe Domain Users 43671 Jul 10 13:27 Amplicons.bed
drwx------+ 1 cmccabe Domain Users 0 Jul 10 13:22 bin
drwx------+ 1 cmccabe Domain Users 0 Jul 10 13:22 data
drwx------+ 1 cmccabe Domain Users 0 Jul 10 13:22 docs
drwx------+ 1 cmccabe Domain Users 0 Jul 10 13:22 genomes
-rwx------+ 1 cmccabe Domain Users 484 Jul 10 09:40 hg19_genome.txt
-rwx------+ 1 cmccabe Domain Users 17988 Nov 3 2012 LICENSE
-rwx------+ 1 cmccabe Domain Users 6693 Nov 3 2012 Makefile
drwx------+ 1 cmccabe Domain Users 0 Jul 10 13:22 obj
-rwx------+ 1 cmccabe Domain Users 1505 Nov 3 2012 README.rst
-rwx------+ 1 cmccabe Domain Users 32293 Nov 3 2012 RELEASE_HISTORY
drwx------+ 1 cmccabe Domain Users 0 Jul 10 13:22 scripts
drwx------+ 1 cmccabe Domain Users 0 Jul 10 13:22 src
drwx------+ 1 cmccabe Domain Users 0 Jul 10 13:22 test

cmccabe@DTV-L2231M5J /cygdrive/c/Users/cmccabe/Desktop/Ion_Torrent_ Software/bedtools-2.17.0
$ head -3 Amplicons.bed | od -c
0000000 c h r 1 \t 2 1 6 0 2 9 0 \t 2 1 6
0000020 0 4 7 5 \t S K I \t . \t A M P L 2
0000040 6 8 8 8 2 8 3 5 2 \n c h r 1 \t 2
0000060 1 6 0 4 8 0 \t 2 1 6 0 6 3 4 \t S
0000100 K I \t . \t A M P L 2 6 8 8 8 2 9
0000120 5 3 0 \n c h r 1 \t 2 1 6 0 6 3 2
0000140 \t 2 1 6 0 7 3 8 \t S K I \t . \t A
0000160 M P L 2 6 8 8 8 2 8 0 5 8 \n
0000176

cmccabe@DTV-L2231M5J /cygdrive/c/Users/cmccabe/Desktop/Ion_Torrent_ Software/bedtools-2.17.0
$ head -3 hg19_genome.txt | od -c
0000000 c h r 1 \t 2 4 9 , 2 5 0 , 6 2 1
0000020 \t \t \n c h r 2 \t 2 4 3 , 1 9 9 ,
0000040 3 7 3 \t \t \t \n c h r 3 \t 1 9 8 ,
0000060 0 2 2 , 4 3 0 \t \t \t \n
0000073
Thank you.

[sdriscoll]

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.

I just read through this thread and while I don't have anything to offer I did notice that the command call was switched around again in this post (bamToBed instead of bedToBam).

[GenoMax]

Looks like you have some extra tabs in the hg19_genome.txt file.

Can you try the genomes file supplied by bedtools in "genomes\human.hg19.genome"?

$ bin/bamToBed -i Amplicons.bed -g genomes/human.hg19.genome > Amplicons.bam

[cmccabe]

bed2bam

cmccabe@DTV-L2231M5J ~
$ cd "C:\Users\cmccabe\Desktop\Ion_Torrent_ Software\bedtools-2.17.0"

cmccabe@DTV-L2231M5J /cygdrive/c/Users/cmccabe/Desktop/Ion_Torrent_ Software/bedtools-2.17.0
$ bin/bedToBam -i Amplicons.bed -g genomes/human.hg19.genome > Amplicons.bam

The resulting BAM file is 0kb

Amplicons.bed: (~43kb after dos2unix)
chr1 2160290 2160475 SKI . AMPL2688828352
chr1 2160480 2160634 SKI . AMPL2688829530
chr1 2160632 2160738 SKI . AMPL2688828058

Thanks.

[GenoMax]

I am fresh out of ideas as to what to do next.

Do you have a colleague who has access to a Mac/unix machine? Perhaps it would be best to try this conversion there.

[Heisman]

Maybe the first lines of your Amplicons.bed are ok but later lines aren't? Could you try "head -2 Amplicons.bed > Amplicons_3lines.bed" and then run it with the new file?

Also try to run the command without the "> Amplicons.bam" part and see if you get any output directly to the screen.

If that doesn't work, try to run "mergeBed" instead of "bedToBam" like this: "bin/mergeBed -i Amplicons.bed" and see if something outputs to the screen, just to make sure there isn't something specifically weird with the "bedToBam" program.

[Heisman]

I'm with GenoMax though; really wish I could teleport to your computer to try to figure this out.

[cmccabe]

bed2bam

I am in the process of using ubuntu 12.0.4 and at the point of compiling the binaries. I have the gcc compilier but what is the command for the zlib and python. I think those where the 3 things needed. Thanks.

[GenoMax]

Start making sure that you have the compilation essentials installed (make, gcc etc)

sudo apt-get install build-essential

and then get the rest

sudo apt-get install zlib zlib-devel python

[cmccabe]

bed2Bam

When I use the code below I get unable to locate zlib-devel

sudo apt-get install zlib zlib-devel python

Thank you very much.

[GenoMax]

Try this instead of the previous zlib:

sudo apt-get install zlib1g zlib1g-dev

[cmccabe]

Bed2Bam

Bedtools 2.17 is compilied on Ubuntu and the command:

bin/bamToBed -i Amplicons.bed -g genomes/human.hg19.genome > Amplicons.bam does run but there is an error extracting the gz file and it is 0 bytes. Thanks.