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Forum: Bioinformatics 03-17-2014, 11:36 AM
Replies: 1
Views: 2,286
Posted By quinlana
Please have a look at the following bedtools...

Please have a look at the following bedtools protocol:
https://github.com/arq5x/bedtools-protocols/blob/master/bedtools.md#ap2b-assessing-coverage-in-exome-capture-experiments-
Forum: Bioinformatics 02-08-2014, 06:04 PM
Replies: 0
Views: 1,065
Posted By quinlana
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, 01:09 PM
Replies: 1
Views: 1,918
Posted By quinlana
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, 06:19 AM
Replies: 0
Views: 975
Posted By quinlana
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, 04:31 AM
Replies: 5
Views: 2,790
Posted By quinlana
Have a look at the "bedtools makewindows" command...

Have a look at the "bedtools makewindows" command in bedtools v2.15.0.

Examples:

# Divide the human genome into windows of 1MB:
$ bedtools makewindows -g hg19.txt -w 1000000
chr1 0...
Forum: Bioinformatics 01-04-2012, 07:01 AM
Replies: 4
Views: 2,542
Posted By quinlana
Why not use those tools and intersect the file to...

Why not use those tools and intersect the file to itself?
Forum: Bioinformatics 09-29-2011, 04:53 PM
Replies: 10
Views: 3,351
Posted By quinlana
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, 05:23 PM
Replies: 2
Views: 6,452
Posted By quinlana
If you type "coverageBed -h", the last few lines...

If you type "coverageBed -h", the last few lines describe the output format.

Default Output:
After each entry in B, reports:
1) The number of features in A that overlapped the B...
Forum: Bioinformatics 04-15-2011, 03:43 AM
Replies: 13
Views: 7,487
Posted By quinlana
You can do this very easily with the BEDTools...

You can do this very easily with the BEDTools fastaFromBed command. Also, here is a thread covering other solutions:
...
Forum: Bioinformatics 04-14-2011, 10:41 AM
Replies: 4
Views: 5,204
Posted By quinlana
Currently, sorting makes no difference for...

Currently, sorting makes no difference for intersect or coverage.
Forum: Academic/Non-Profit Jobs 03-24-2011, 06:41 AM
Replies: 0
Views: 1,848
Posted By quinlana
Postdoc/Research Associate in Computational Genomics at the Univ. of Virginia

I would like to point you to an open research position in the Quinlan Laboratory at the University of Virginia's Center for Public Health Genomics. We are looking for motivated scientists with...
Forum: Bioinformatics 02-10-2011, 04:48 AM
Replies: 11
Views: 3,176
Posted By quinlana
Just add a grep -v "_random" after the output of...

Just add a grep -v "_random" after the output of genomeCoverageBed to filter any intervals arising from the "random" chroms.
Forum: Bioinformatics 02-09-2011, 11:59 AM
Replies: 11
Views: 3,176
Posted By quinlana
I'm not sure why you wouldn't be using the same...

I'm not sure why you wouldn't be using the same .fai as the header in your BAM, but in this case you could just make a new "genome" file from your BAM header.


samtools view -H [BAM] | grep "@SQ"...
Forum: Bioinformatics 02-09-2011, 06:17 AM
Replies: 29
Views: 13,072
Posted By quinlana
Assuming you have used BWA for Tier 1, your Tier...

Assuming you have used BWA for Tier 1, your Tier 1 BAM file should be in "query order". That is, the order of the alignments in the BAM file should be in the order of the input FASTQ files. Using...
Forum: Bioinformatics 02-09-2011, 05:51 AM
Replies: 11
Views: 3,176
Posted By quinlana
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, 03:43 PM
Replies: 4
Views: 23,235
Posted By quinlana
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, 10:20 AM
Replies: 5
Views: 3,336
Posted By quinlana
Your issue is likely that the time() function has...

Your issue is likely that the time() function has granularity to the second. If you make multiple calls to you program in the same second, the results will be identical. The following will seed...
Forum: Bioinformatics 11-29-2010, 05:35 PM
Replies: 4
Views: 11,232
Posted By quinlana
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, 07:45 AM
Replies: 4
Views: 1,601
Posted By quinlana
Could you please provide a more concrete example...

Could you please provide a more concrete example of what you want? For instance, maybe a toy file with your expected result and how it differs from what you get with intersect or merge? I think it's...
Forum: Bioinformatics 10-07-2010, 03:23 PM
Replies: 14
Views: 5,223
Posted By quinlana
There should be two files: one with the sites of...

There should be two files: one with the sites of polymorphism (the one you show here) and another with the genotypes at said sites. Look for *.genotypes.* or something like that.
Forum: Bioinformatics 10-07-2010, 12:02 PM
Replies: 23
Views: 12,686
Posted By quinlana
<shameless plug> Note that BEDTools has a tool...

<shameless plug>
Note that BEDTools has a tool called bedToIGV that will automatically create an IGV batch script from a BED, GFF, or VCF file.
</shameless plug>
Forum: Bioinformatics 10-02-2010, 05:10 PM
Replies: 4
Views: 1,642
Posted By quinlana
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, 05:07 AM
Replies: 8
Views: 5,864
Posted By quinlana
That is odd. Could you post the command you used...

That is odd. Could you post the command you used and the output?
Section 5.9.6 of the manual (http://bedtools.googlecode.com/files/BEDTools-User-Manual.v4.pdf) illustrates the way the output should...
Forum: Bioinformatics 09-28-2010, 04:55 AM
Replies: 8
Views: 5,864
Posted By quinlana
Use the -d option for per base coverage. ...

Use the -d option for per base coverage. Available in version 2.9 and later.
Aaron
Forum: Bioinformatics 09-21-2010, 05:25 PM
Replies: 0
Views: 2,782
Posted By quinlana
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....
Showing results 1 to 25 of 119

 


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