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Search: Posts Made By: Jose Blanca
Forum: Bioinformatics 04-29-2013, 12:01 AM
Replies: 24
Views: 16,329
Posted By Jose Blanca
The newest sff_extract can not create the...

The newest sff_extract can not create the traceinfo xml file. We have to add it to the new sff_extract, we add it to the TODO. If you need that functionallity you can use the old sff_extract:...
Forum: Bioinformatics 04-25-2013, 01:07 AM
Replies: 24
Views: 16,329
Posted By Jose Blanca
Which python version are you using? Are you using...

Which python version are you using? Are you using python 2.7? It's a strange problem because that missing module belongs to the standard library.
The newest sff_extract is now included in a package...
Forum: Bioinformatics 01-17-2013, 11:38 PM
Replies: 24
Views: 16,329
Posted By Jose Blanca
It's a python script, just run it with: ...

It's a python script, just run it with:

python sff_extract
Forum: Bioinformatics 01-06-2013, 11:59 PM
Replies: 24
Views: 16,329
Posted By Jose Blanca
Don't worry I'm on the thread too, we'll talk...

Don't worry I'm on the thread too, we'll talk there. In the mean time you can use the old sff_extract.
Regards,

Jose Blanca
Forum: Bioinformatics 01-03-2013, 01:52 AM
Replies: 24
Views: 16,329
Posted By Jose Blanca
You would had to trim the reads before feeding...

You would had to trim the reads before feeding them to Mira. I guess tha the latest version do not require the notraceinfo, but I recommend to you to ask in the Mira mailing list, because I haven't...
Forum: Bioinformatics 01-02-2013, 05:10 AM
Replies: 24
Views: 16,329
Posted By Jose Blanca
From the Mira mailing list: If you...

From the Mira mailing list:



If you trim the reads I think that the xml file is irrelevant, but I would ask in the Mira mailing list just in case.
Forum: Bioinformatics 01-02-2013, 12:31 AM
Replies: 24
Views: 16,329
Posted By Jose Blanca
It seems that you are using the new sff_extract...

It seems that you are using the new sff_extract included in the seq_crumbs package. This new sff_extract has a new interface and it has changed its behaviour a little. I recommend you to use this new...
Forum: Bioinformatics 06-14-2011, 11:51 PM
Replies: 28
Views: 7,918
Posted By Jose Blanca
I would recommend to to a quality boxplot to...

I would recommend to to a quality boxplot to understand how every run went. You have an example of a boxplot here:
...
Forum: Bioinformatics 06-14-2011, 11:42 PM
Replies: 8
Views: 3,055
Posted By Jose Blanca
We also have som documentation for our students:...

We also have som documentation for our students: http://bioinf.comav.upv.es/courses/sequence_analysis/
Forum: Bioinformatics 06-12-2011, 11:50 PM
Replies: 28
Views: 7,918
Posted By Jose Blanca
I think that I have fixed the problem. The fix is...

I think that I have fixed the problem. The fix is included in the psubprocess that I have just released, could you try to reinstall psubprcess with this version...
Forum: Bioinformatics 06-10-2011, 05:58 AM
Replies: 28
Views: 7,918
Posted By Jose Blanca
Take a look at the lucy documentation, because...

Take a look at the lucy documentation, because you have to use their parameters.
Forum: Bioinformatics 06-09-2011, 07:42 AM
Replies: 28
Views: 7,918
Posted By Jose Blanca
Are you sure the file is in there? could it be a...

Are you sure the file is in there? could it be a problem with the letter case? In unix the case matter Pair01_fastq_format.fastq and pair01_fastq_format.fastq would be different files.
Can you run...
Forum: Bioinformatics 06-09-2011, 06:22 AM
Replies: 28
Views: 7,918
Posted By Jose Blanca
Sorry, I have not explained myself well enough. ...

Sorry, I have not explained myself well enough.
clean_reads uses two different algorithms for quality trimming. One for long reads (lucy (http://lucy.sourceforge.net/)) and a different one for short...
Forum: Bioinformatics 06-08-2011, 11:31 PM
Replies: 28
Views: 7,918
Posted By Jose Blanca
You can not use the --qual_thrshold parameter for...

You can not use the --qual_thrshold parameter for long reads (sanger or 454). I have to explain that in the documentation a little. For the long reads we trim the bad quality regions by using lucy so...
Forum: Bioinformatics 06-08-2011, 05:41 AM
Replies: 28
Views: 7,918
Posted By Jose Blanca
In mac it won't work, because the binaries shiped...

In mac it won't work, because the binaries shiped inside clean_reads are only for linux.
Regarding the linux problem, it's a malformed command line. It should be:
--qual_threshold
instead of:...
Forum: Bioinformatics 06-08-2011, 03:53 AM
Replies: 28
Views: 7,918
Posted By Jose Blanca
I would need more information. A segmentation...

I would need more information. A segmentation fault is quite a strange error in a python program. could you send me the output?
Forum: Bioinformatics 06-02-2011, 11:43 PM
Replies: 3
Views: 4,782
Posted By Jose Blanca
Thanks for the tips, I'll look into them. I...

Thanks for the tips, I'll look into them. I didin't know about sim4db and genome threader. sim4db seems interesting, the only problem is that it doesn't support sam output.
exonerate is nice, but it...
Forum: Bioinformatics 06-01-2011, 11:58 PM
Replies: 3
Views: 4,782
Posted By Jose Blanca
mapping ESTs to genome

Hi:

I have some 454 and sanger reads that I want to map to a genome. I've tried with gmap. gmap find the introns, but tends to do a lot of small misalignments inside the exons that end up as false...
Forum: Bioinformatics 05-31-2011, 11:54 PM
Replies: 28
Views: 7,918
Posted By Jose Blanca
We have done our own read cleaning pipeline. It...

We have done our own read cleaning pipeline. It works for us, so we have made it available just in case it could be of any use to other people. It is called clean_reads...
Forum: Bioinformatics 05-22-2011, 11:48 PM
Replies: 6
Views: 3,639
Posted By Jose Blanca
gmap can align 454 ESTs against a genome taking...

gmap can align 454 ESTs against a genome taking into account the introns.
Forum: Bioinformatics 05-17-2011, 11:44 PM
Replies: 2
Views: 2,667
Posted By Jose Blanca
It seems that the problem is related to your...

It seems that the problem is related to your different python versions. You have at least python2.6 and python 2.7. Each python version has its own libraries so when you have installed matplotlib...
Forum: Bioinformatics 03-16-2011, 01:22 AM
Replies: 1
Views: 1,955
Posted By Jose Blanca
We do something similar. ...

We do something similar.

http://bioinf.comav.upv.es/ngs_backbone/

Regards.
Forum: Bioinformatics 03-16-2011, 01:15 AM
Replies: 3
Views: 4,725
Posted By Jose Blanca
We usually merge bam files for GATK. Our code is...

We usually merge bam files for GATK. Our code is exposed in a pipeline (http://bioinf.comav.upv.es/ngs_backbone/), but if you like python you could use the underlying library...
Forum: Bioinformatics 03-16-2011, 01:12 AM
Replies: 7
Views: 2,732
Posted By Jose Blanca
We do a little workshop for our students, the...

We do a little workshop for our students, the materials could be of some use to you.

http://bioinf.comav.upv.es/courses/sequence_analysis/

Regards.
Forum: Bioinformatics 03-16-2011, 01:04 AM
Replies: 5
Views: 7,110
Posted By Jose Blanca
We work with mixed samples coming from different...

We work with mixed samples coming from different individuals and we have developed an SNP caller to work with them. You can take a look at:

http://bioinf.comav.upv.es/ngs_backbone/

Best...
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