Originally posted by cmccabe
View Post
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
$ 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
Comment
-
Originally posted by cmccabe View PostWhat 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.
Comment
-
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)?Last edited by GenoMax; 07-10-2013, 06:29 AM.
Comment
-
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.
Comment
Latest Articles
Collapse
-
by seqadmin
While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...-
Channel: Articles
06-06-2024, 07:15 AM -
-
by seqadmin
Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.
Somatic Genomics
“We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...-
Channel: Articles
05-24-2024, 01:16 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 08:58 AM
|
0 responses
9 views
0 likes
|
Last Post
by seqadmin
Yesterday, 08:58 AM
|
||
Started by seqadmin, 06-12-2024, 02:20 PM
|
0 responses
15 views
0 likes
|
Last Post
by seqadmin
06-12-2024, 02:20 PM
|
||
Started by seqadmin, 06-07-2024, 06:58 AM
|
0 responses
182 views
0 likes
|
Last Post
by seqadmin
06-07-2024, 06:58 AM
|
||
Started by seqadmin, 06-06-2024, 08:18 AM
|
0 responses
231 views
0 likes
|
Last Post
by seqadmin
06-06-2024, 08:18 AM
|
Comment