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Search: Posts Made By: fpepin
Forum: Bioinformatics 07-27-2011, 01:21 PM
Replies: 6
Views: 8,736
Posted By fpepin
Not quite. They haven't updated the BWA...

Not quite. They haven't updated the BWA documentation to say that that 1.3+ should be 1.3-1.7. With 1.8, just don't use the -I and you'll be doing just fine.
Forum: Bioinformatics 07-15-2011, 02:15 PM
Replies: 6
Views: 2,977
Posted By fpepin
Java Runtime.exec(String command) should inherit...

Java Runtime.exec(String command) should inherit the environment of the parent processes unless you overwrite it.

Two options for figure out what's wrong:
1- look at the output of:...
Forum: Bioinformatics 07-15-2011, 01:59 PM
Replies: 4
Views: 2,895
Posted By fpepin
samtools is complaining about not finding an...

samtools is complaining about not finding an index file in the same directory: 5673_5_t8.sortedbam.bam.bai. Is one there?

If not, then you want to create one using:
samtools index...
Forum: Bioinformatics 07-08-2011, 05:01 PM
Replies: 3
Views: 4,719
Posted By fpepin
I'm actually having the same problem as well....

I'm actually having the same problem as well. CleanSam doesn't help in this case. Picard's ValidateSamFile does show multiple errors that I think are related:

Mate unmapped flag does not match...
Forum: Bioinformatics 06-14-2011, 10:49 PM
Replies: 5
Views: 5,208
Posted By fpepin
I'm not an expert, but that does sound reasonable...

I'm not an expert, but that does sound reasonable (and very close to what I have). I also call the indel discovery tool before the realignment to get additional regions to focus on.

I use Picard...
Forum: Bioinformatics 06-14-2011, 06:40 PM
Replies: 5
Views: 3,437
Posted By fpepin
I hadn't understood the question was about the...

I hadn't understood the question was about the script, not bwa.

I haven't read that book but I've heard good things about it.

You can do it in the shell fairly easily too:

for i in file*
do...
Forum: Bioinformatics 06-14-2011, 05:14 PM
Replies: 5
Views: 3,437
Posted By fpepin
How about giving us the error message that you're...

How about giving us the error message that you're getting? What if you just run one of them in isolation? It's hard to guess what the problem is as we have no idea what your environment and files are.
Forum: Bioinformatics 06-14-2011, 04:47 PM
Replies: 5
Views: 5,208
Posted By fpepin
Is this what you have in mind?...

Is this what you have in mind? http://www.broadinstitute.org/gsa/wiki/index.php/Local_realignment_around_indels

Score recalibration can be found at...
Forum: Bioinformatics 06-14-2011, 03:39 PM
Replies: 3
Views: 2,606
Posted By fpepin
Are these matched normals or you have 16...

Are these matched normals or you have 16 individuals in all?

Running in all together would get you an average of everything, which would be a bad idea. Unless you think that your SNP of interest...
Forum: Bioinformatics 06-14-2011, 03:15 PM
Replies: 3
Views: 2,840
Posted By fpepin
Yes. This is with a GAIIx, not a high-seq,...

Yes.

This is with a GAIIx, not a high-seq, but I have the following files appearing:
Basecalling_Netcopy_complete.txt

Depending of what information you want, this might also be of interest:...
Forum: Bioinformatics 05-03-2011, 11:49 AM
Replies: 4
Views: 4,035
Posted By fpepin
No, I haven't been able to figure it out and I...

No, I haven't been able to figure it out and I got side-tracked by other problems. I'll see if I can spend a bit more time to go to the bottom of it.
Forum: Introductions 03-24-2011, 03:33 PM
Replies: 1
Views: 1,537
Posted By fpepin
Welcome Valeria, as for your question, I'll...

Welcome Valeria,

as for your question, I'll give you the same answer I got when I asked my first question on this thread: go to the bioinformatics forum and ask there.

That's where people will...
Forum: Bioinformatics 03-24-2011, 03:08 PM
Replies: 5
Views: 4,836
Posted By fpepin
I'd say whatever makes you most comfortable. I'm...

I'd say whatever makes you most comfortable. I'm fond of OS X as a desktop machine because I can also use MS office & Adobe illustrator and such. The Mac Pros that you'd want to do serious analysis...
Forum: Bioinformatics 03-13-2011, 11:15 PM
Replies: 4
Views: 4,035
Posted By fpepin
Any suggestion on how to find the reads that are...

Any suggestion on how to find the reads that are causing the problem?

samtools view does give out the beginning of the sam file so it's not every read that's problematic, but I'm not quite sure...
Forum: Bioinformatics 03-13-2011, 03:34 AM
Replies: 4
Views: 4,035
Posted By fpepin
Exclamation bwa bug (?) leading to samtools segfault

Hi everyone,

In trying what might be a bit of premature optimization, I'm hitting an unfortunate segmentation fault in samtools.

This is with an illumina GAIIx. The original pipeline ungzipped...
Forum: Bioinformatics 03-10-2011, 12:23 AM
Replies: 3
Views: 2,123
Posted By fpepin
Maybe you could give us some more information as...

Maybe you could give us some more information as to what your data is supposed to represent? If you got the data from GEO, then you should be able to find some documentation about it. Not knowing the...
Forum: Service Providers 02-18-2011, 05:40 PM
Replies: 3
Views: 4,961
Posted By fpepin
Hi magcha, would you mind saying which are...

Hi magcha,

would you mind saying which are the NGS-specific companies you have in mind? We're looking at the same thing right now and I'm curious if there are obvious cases that we've missed.
...
Forum: Bioinformatics 02-18-2011, 01:32 PM
Replies: 82
Views: 32,727
Posted By fpepin
I've seen my share of wet labs that have students...

I've seen my share of wet labs that have students bring in their own personal laptops and not even a backup system, and the department wasn't much savvier either.

It's doable, but I know I'd be...
Forum: Bioinformatics 02-18-2011, 12:36 PM
Replies: 82
Views: 32,727
Posted By fpepin
Not everyone has the resources or expertise to...

Not everyone has the resources or expertise to set up (and maintain!) a DAS server or another type of repository. This is going to be exacerbated as costs go down and every lab is going to be doing...
Forum: Bioinformatics 02-17-2011, 12:22 AM
Replies: 82
Views: 32,727
Posted By fpepin
I think we are talking about the same thing. My...

I think we are talking about the same thing. My point is that you could have significant savings in storage requirement by basing it off a reference when available.

The quality score are indeed a...
Forum: Bioinformatics 02-16-2011, 05:41 PM
Replies: 82
Views: 32,727
Posted By fpepin
I'm talking of using it as a compression feature....

I'm talking of using it as a compression feature. Imagine a toy example where 90% of the reads map exactly to the reference (no SNPs/indels) and the rest doesn't map at all. A position and a length...
Forum: Bioinformatics 02-16-2011, 04:46 PM
Replies: 82
Views: 32,727
Posted By fpepin
But you can do that losslessly as well if you...

But you can do that losslessly as well if you have the same reference genome: store start position, end position, differences with reference.

The still leaves the non-aligned reads and the quality...
Forum: Bioinformatics 02-11-2011, 01:53 PM
Replies: 17
Views: 7,836
Posted By fpepin
Thanks Micheal, I'll update my pipeline then. ...

Thanks Micheal, I'll update my pipeline then.

I also talked to more people about this issue and the answer is that this is a well-known issue when you have a specific tetramer (CCGG, if I remember...
Forum: Bioinformatics 02-10-2011, 10:51 AM
Replies: 17
Views: 7,836
Posted By fpepin
Bruins:This is 2 lanes per sample. I haven't...

Bruins:This is 2 lanes per sample. I haven't checked the results from the individual lanes in my haste to get results, but I'm running it now.

Also, the runs are basically all cancer-related. I...
Forum: Bioinformatics 02-09-2011, 04:55 PM
Replies: 17
Views: 7,836
Posted By fpepin
This is also using GATK (java -jar...

This is also using GATK (java -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -pl SOLEXA ...) for the variant calling. Is samtools likely to be different?

Could it be that slightly more stringent...
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