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?
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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.
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Originally posted by cmccabe View PostI 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./* Shawn Driscoll, Gene Expression Laboratory, Pfaff
Salk Institute for Biological Studies, La Jolla, CA, USA */
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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.
Comment
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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.
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