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Search: Posts Made By: pmaugeri
Forum: Bioinformatics 12-22-2011, 01:35 AM
Replies: 17
Views: 73,396
Posted By pmaugeri
@Alex, I just ended another round of indels...

@Alex,

I just ended another round of indels calling against several sets of simulated data. In brief I simulated sets of reads for chromosome 20 at four different coverages (5x, 11x, 22x, 44x).
...
Forum: Bioinformatics 12-16-2011, 01:10 AM
Replies: 17
Views: 73,396
Posted By pmaugeri
@Alex Renwick: I am not sure whether it helps to...

@Alex Renwick: I am not sure whether it helps to do realignment around known indels here (I guess you refer to the steps described in...
Forum: Bioinformatics 12-12-2011, 04:06 AM
Replies: 17
Views: 73,396
Posted By pmaugeri
Thank you Sir! I added your comment into the post.

Thank you Sir! I added your comment into the post.
Forum: Bioinformatics 12-12-2011, 12:21 AM
Replies: 17
Views: 73,396
Posted By pmaugeri
Thanks Heisman for your comment. If I have...

Thanks Heisman for your comment.

If I have understood correctly you propose to generate the .bam file in an uncompressed format:

bwa sampe -f out.sam -r '@RG\tID:foo\tSM:bar'...
Forum: Bioinformatics 12-09-2011, 01:32 PM
Replies: 17
Views: 73,396
Posted By pmaugeri
I confirm your suspicion: it is not that easy to...

I confirm your suspicion: it is not that easy to find a data sets suitable for practicing. Simulated data sets is a good complementary source of data.

Of course you have data sets from 1000g...
Forum: Bioinformatics 12-09-2011, 12:06 PM
Replies: 17
Views: 73,396
Posted By pmaugeri
wow :-O Thanks for taking the time to read it...

wow :-O
Thanks for taking the time to read it and for your very interesting comments. I will modify the post accordingly.

I believe that wgsim is limited compared to maq simulator and I plan to...
Forum: Bioinformatics 12-09-2011, 11:37 AM
Replies: 17
Views: 73,396
Posted By pmaugeri
Pipeline to simulate short reads and call indels

Hi

http://biotechies.blogspot.com/2011/12/pipelines-to-simulate-and-detect-indels.html is a kind of howto for doing the following pipeline:

1. simulate short reads (wgsim)

2. align short...
Forum: Bioinformatics 12-02-2011, 12:35 AM
Replies: 3
Views: 2,469
Posted By pmaugeri
Is there a way to export/convert the wgsim output...

Is there a way to export/convert the wgsim output to a VCF file?
Thanks
Forum: Bioinformatics 10-27-2011, 02:37 AM
Replies: 2
Views: 3,463
Posted By pmaugeri
I found a quick solution for this errror: the...

I found a quick solution for this errror: the samtools binary I was using was installed through apt-get as a binary package in my ubuntu distro. I removed it and compiled from latest source code...
Forum: Bioinformatics 10-24-2011, 08:20 AM
Replies: 2
Views: 3,463
Posted By pmaugeri
samtools tview produces "Floating point exception" on big file?

Hi,

I'm getting a "Floating point exception" trying to run the following:

samtools tview NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam human_g1k_v37.fasta

Can you confirm that this error...
Forum: Pacific Biosciences 09-27-2011, 04:08 AM
Replies: 2
Views: 2,896
Posted By pmaugeri
The meaning of "realtime" here

Hi

I read the product description of the instrument:

"The PacBio RS system conducts, monitors and analyzes single molecule, realtime (SMRT™) sequencing reactions.
[...]
These signals are...
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