Forum: Bioinformatics
03-17-2014, 12:36 PM
|
|
Replies: 1
Views: 2,406
|
|
Forum: Bioinformatics
02-08-2014, 07:04 PM
|
|
Replies: 0
Views: 1,127
bedtools version 2.19.0
We just posted version 2.19.0 of bedtools. The intersect tool is ~5x faster than in 2.17, and the map tool is ~3x faster. Multiple bugs fixes and new functionality.
Details of the release:...
|
|
Forum: Bioinformatics
11-03-2012, 02:09 PM
|
|
Replies: 1
Views: 2,017
bedtools version 2.17.0
My lab has just released version 2.17 of bedtools. This release includes a few important algorithm improvements, a new Jaccard tool for measuring relationships between interval (BED, VCF, GFF) files,...
|
|
Forum: Academic/Non-Profit Jobs
06-18-2012, 07:19 AM
|
|
Replies: 0
Views: 1,059
Genomics Software Engineer: Quinlan Lab @ UVA
My laboratory is seeking an experienced, creative, and highly motivated programmer / software engineer to fill a Scientific Programmer position in our computational genomics research group at the...
|
|
Forum: Bioinformatics
02-19-2012, 05:31 AM
|
|
Replies: 5
Views: 2,920
|
|
Forum: Bioinformatics
01-04-2012, 08:01 AM
|
|
Replies: 4
Views: 2,667
|
|
Forum: Bioinformatics
09-29-2011, 05:53 PM
|
|
Replies: 10
Views: 3,547
If you install bedtools...
If you install bedtools (http://bedtools.googlecode.com), you could use the "mergeBed" program to merge overlapping reads on the same strand as follows:
bamToBed -i aln.bam | mergeBed -i stdin -s >...
|
|
Forum: Bioinformatics
07-01-2011, 06:23 PM
|
|
Replies: 2
Views: 6,650
|
|
Forum: Bioinformatics
04-15-2011, 04:43 AM
|
|
Replies: 13
Views: 7,822
|
|
Forum: Bioinformatics
04-14-2011, 11:41 AM
|
|
Replies: 4
Views: 5,422
|
|
Forum: Academic/Non-Profit Jobs
03-24-2011, 07:41 AM
|
|
Replies: 0
Views: 1,946
|
|
Forum: Bioinformatics
02-10-2011, 05:48 AM
|
|
Replies: 11
Views: 3,343
|
|
Forum: Bioinformatics
02-09-2011, 12:59 PM
|
|
Replies: 11
Views: 3,343
|
|
Forum: Bioinformatics
02-09-2011, 07:17 AM
|
|
Replies: 29
Views: 13,533
|
|
Forum: Bioinformatics
02-09-2011, 06:51 AM
|
|
Replies: 11
Views: 3,343
genomeCoverageBed in the BEDTools...
genomeCoverageBed in the BEDTools (http://bedtools.googlecode.com) package will do this for you.
The "-d" option will report depth at every base (perhaps excessive). The -bga option will create a...
|
|
Forum: Bioinformatics
01-28-2011, 04:43 PM
|
|
Replies: 4
Views: 24,466
The awesome power of awk and sed.
sed -e...
The awesome power of awk and sed.
sed -e 's/chr//' file.vcf | awk '{OFS="\t"; if (!/^#/){print $1,$2-1,$2,$4"/"$5,"+"}}'
where you replace "file.vcf" with your file. Note this uses 0-based...
|
|
Forum: Bioinformatics
01-28-2011, 11:20 AM
|
|
Replies: 5
Views: 3,581
|
|
Forum: Bioinformatics
11-29-2010, 06:35 PM
|
|
Replies: 4
Views: 12,251
Similar to adamdeluca's suggestion, here is...
Similar to adamdeluca's suggestion, here is another simple awk solution. Note that the ">>" creates and appends to files named CHROM.bed, where CHROM is column 1 of the bed input bed file (in this...
|
|
Forum: Bioinformatics
11-08-2010, 08:45 AM
|
|
Replies: 4
Views: 1,676
|
|
Forum: Bioinformatics
10-07-2010, 04:23 PM
|
|
Replies: 14
Views: 5,384
|
|
Forum: Bioinformatics
10-07-2010, 01:02 PM
|
|
Replies: 23
Views: 13,060
|
|
Forum: Bioinformatics
10-02-2010, 06:10 PM
|
|
Replies: 4
Views: 1,727
At first glance, I think you might want to...
At first glance, I think you might want to double-check your work. This seemed quite odd to me, so I downloaded Tophat for grins. tophat.py ends at line 1855. I suspect that you have duplicated...
|
|
Forum: Bioinformatics
09-28-2010, 06:07 AM
|
|
Replies: 8
Views: 6,011
|
|
Forum: Bioinformatics
09-28-2010, 05:55 AM
|
|
Replies: 8
Views: 6,011
|
|
Forum: Bioinformatics
09-21-2010, 06:25 PM
|
|
Replies: 0
Views: 2,887
BEDTools version 2.10.0
Hi all,
I just posted version 2.10.0. Below are the highlights including a new tool and some useful new features.
http://code.google.com/p/bedtools/
Best,
Aaron
New tools
1....
|
