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Search: Posts Made By: brentp
Forum: Bioinformatics 01-24-2015, 07:14 PM
Replies: 2
Views: 1,098
Posted By brentp
import cruzdb g = cruzdb.Genome('hg19') ...

import cruzdb

g = cruzdb.Genome('hg19')
g.bin_query('refGene', 'chr1', 1234567, 1234568).all()
Forum: Bioinformatics 09-02-2014, 12:06 PM
Replies: 649
Views: 151,063
Posted By brentp
here are the alignments that I get with bwa-meth...

here are the alignments that I get with bwa-meth for that read-pair that you extracted:
...
Forum: Bioinformatics 09-02-2014, 08:59 AM
Replies: 649
Views: 151,063
Posted By brentp
kevinrue, can you send the output of grep...

kevinrue, can you send the output of

grep -A4 HWI-D00238R:175:H8RA2ADXX:1:1216:1567:36545 $FQ

for both ends of your input fastqs?

Also, note that the percentage of output that you are...
Forum: Bioinformatics 09-02-2014, 07:24 AM
Replies: 649
Views: 151,063
Posted By brentp
as far as I can guess, dpryan is correct that...

as far as I can guess, dpryan is correct that what you're seeing is more likely a bwa bug than a bwa-meth bug since I don't mess with the cigar string.
As I told you, you can simply use the...
Forum: Bioinformatics 04-17-2014, 04:01 PM
Replies: 16
Views: 5,374
Posted By brentp
I mean it gives similar and therefore I assume...

I mean it gives similar and therefore I assume sane/correct output.
Forum: Bioinformatics 04-17-2014, 08:06 AM
Replies: 16
Views: 5,374
Posted By brentp
by the way, in the bwa-meth repository, there is...

by the way, in the bwa-meth repository, there is a script for extracting methylation call from any sorted bam file regardless of it's origin (aligner). It is here:
...
Forum: Bioinformatics 04-17-2014, 08:03 AM
Replies: 16
Views: 5,374
Posted By brentp
I would have to do some tests on 75 base reads...

I would have to do some tests on 75 base reads but indeed, bwa mem will work fine on them, I just wanted to be conservative in the recommendation. I assume that it would be fine. For you problem with...
Forum: Bioinformatics 04-01-2014, 01:50 PM
Replies: 4
Views: 1,174
Posted By brentp
Thanks Devon, I'll look into that more. I knew...

Thanks Devon, I'll look into that more. I knew that BiSeq used the betaregression, but didn't think about the details.

Some others have also suggested that I look into plink/seq or pseq.
Forum: Bioinformatics 03-31-2014, 08:50 AM
Replies: 4
Views: 1,174
Posted By brentp
DESeq/EdgeR on counts of reads supporting variant

Is there precedent for and/or is it sensible to use DESeq or EdgeR to model counts of reads supporting variants in order to get significance?

For example, suppose I have 10 cases and 10 controls...
Forum: Bioinformatics 03-14-2014, 02:52 PM
Replies: 649
Views: 151,063
Posted By brentp
it does support single-end as well, but yeah,...

it does support single-end as well, but yeah, only directional for now.

glad to see bismark outputting the sorted header, that does simplify things for downstream analyses.

what filtering to...
Forum: Bioinformatics 02-11-2014, 08:58 AM
Replies: 16
Views: 5,374
Posted By brentp
Devon, that's a nice analysis and a good way to...

Devon, that's a nice analysis and a good way to visualize the differences, thanks for trying it on the real data. Would you mind sharing the bison parameters you recommend?

I updated the git repo...
Forum: Bioinformatics 02-08-2014, 06:07 AM
Replies: 16
Views: 5,374
Posted By brentp
I have updated a few of the aligners, including...

I have updated a few of the aligners, including bismark with bowtie2 for the data simulated with the Sherman data with a 1% error rate. I am continuing to check parameter values for other aligners so...
Forum: Bioinformatics 02-05-2014, 06:46 AM
Replies: 16
Views: 5,374
Posted By brentp
Hi Devon, since it's using bwa mem, bwa-meth is...

Hi Devon, since it's using bwa mem, bwa-meth is suited for longer reads. I added a warning in case the user tries to send shorter reads. Let me know if you have problems with 2x100 reads.
Forum: Bioinformatics 02-04-2014, 09:34 AM
Replies: 16
Views: 5,374
Posted By brentp
Devon, that's interesting to hear about...

Devon, that's interesting to hear about gnumap-bs, from their paper, it looks promising, though I hadn't heard about it until recently.

Felix, thanks for the very thorough reply. I will:
1. use...
Forum: Bioinformatics 02-04-2014, 04:36 AM
Replies: 16
Views: 5,374
Posted By brentp
Arrow bwa-meth and bs-seq comparison

Hi All, I have written a simple BS-Seq aligner that wraps bwa mem. It is available from here: https://github.com/brentp/bwa-meth

There is a writeup of it here: http://arxiv.org/abs/1401.1129

In...
Forum: Bioinformatics 12-05-2013, 01:25 PM
Replies: 649
Views: 151,063
Posted By brentp
... and now I see that it already does write...

... and now I see that it already does write directly to bam. thanks.
Forum: Bioinformatics 12-05-2013, 12:47 PM
Replies: 19
Views: 7,684
Posted By brentp
I had to add -lpthread to bias and methylation...

I had to add -lpthread to bias and methylation extractor but it installed fine with openmpi after that.

Thanks.
Forum: Bioinformatics 12-05-2013, 10:31 AM
Replies: 649
Views: 151,063
Posted By brentp
Hi, Bismark is creating a lot of plain-text...

Hi, Bismark is creating a lot of plain-text output--e.g. 16GB of SAM from 4GB of fastq.gz. It would be nice if it output BAM format instead of SAM. Even if it could be forced to output .sam.gz, that...
Forum: Bioinformatics 12-05-2013, 10:26 AM
Replies: 19
Views: 7,684
Posted By brentp
Hi Devon, this seems very interesting. I have...

Hi Devon, this seems very interesting. I have been having trouble with the amount of plain-text output from Bismark.

this seems to require exactly mpich, openmpi doesn't seem to work, is that...
Forum: Bioinformatics 10-14-2013, 04:56 AM
Replies: 6
Views: 4,171
Posted By brentp
Yes, that's a message from the OS. On linux you...

Yes, that's a message from the OS. On linux you can increase that like so: http://www.cyberciti.biz/faq/linux-increase-the-maximum-number-of-open-files/

you could also try reducing the number of...
Forum: Bioinformatics 08-20-2013, 12:22 PM
Replies: 9
Views: 6,642
Posted By brentp
import sys print sum(len(l.rstrip()) for l...

import sys
print sum(len(l.rstrip()) for l in open(sys.argv[1]) if l[0] != ">")
Forum: Bioinformatics 02-19-2013, 06:29 AM
Replies: 7
Views: 1,798
Posted By brentp
use bedtools or pybedtools in python. if your...

use bedtools or pybedtools in python. if your data is in bed format, this will make your script much faster and much simpler.
Forum: Bioinformatics 05-08-2012, 05:24 PM
Replies: 15
Views: 4,076
Posted By brentp
@nbafrank, where's the link so one can wget a tar...

@nbafrank, where's the link so one can wget a tar ball without registering?
Forum: Bioinformatics 04-17-2012, 04:44 AM
Replies: 13
Views: 2,858
Posted By brentp
only if you don't care about keeping around...

only if you don't care about keeping around intermediate files, in case the pipeline adds a step in there or you change some parameters in a later step and don't want to re-run the entire pipeline.
Forum: Bioinformatics 04-17-2012, 04:34 AM
Replies: 13
Views: 2,858
Posted By brentp
Looks pretty useful, could you explain more...

Looks pretty useful, could you explain more about:
http://code.google.com/p/bpipe/wiki/RealPipelineTutorial

where, for example you have:


@Transform("bai")
index = {
exec "samtools...
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