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?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
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.
Comment
-
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 */
Comment
-
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
-
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.
Comment
Latest Articles
Collapse
-
by seqadmin
The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...-
Channel: Articles
05-06-2024, 07:48 AM -
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
04-22-2024, 07:01 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 05-14-2024, 07:03 AM
|
0 responses
16 views
0 likes
|
Last Post
by seqadmin
05-14-2024, 07:03 AM
|
||
Started by seqadmin, 05-10-2024, 06:35 AM
|
0 responses
40 views
0 likes
|
Last Post
by seqadmin
05-10-2024, 06:35 AM
|
||
Started by seqadmin, 05-09-2024, 02:46 PM
|
0 responses
49 views
0 likes
|
Last Post
by seqadmin
05-09-2024, 02:46 PM
|
||
Started by seqadmin, 05-07-2024, 06:57 AM
|
0 responses
41 views
0 likes
|
Last Post
by seqadmin
05-07-2024, 06:57 AM
|
Comment