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Forum: Bioinformatics 06-19-2012, 11:04 AM
Replies: 6
Views: 5,226
Posted By amaer
Thank you very much, I just ran into the exact...

Thank you very much, I just ran into the exact same problem and I was completely puzzled.
I wonder why the mpileup considered all those reads anomalous, do you know what criteria it uses to make...
Forum: Bioinformatics 05-24-2012, 06:14 PM
Replies: 513
Views: 198,824
Posted By amaer
But the read IS mappable (1 mismatch only for 36...

But the read IS mappable (1 mismatch only for 36 bp)! And I can see that when I increase M. I mean, with M 1, it did not map anywhere on the human genome, but it did so when I increased M (keeping...
Forum: Bioinformatics 05-24-2012, 01:00 PM
Replies: 513
Views: 198,824
Posted By amaer
the M option in Bowtie2 beta1.3

Hi,

I have a question about the use of the M parameter in Bowtie2 beta1.3. I understand it's the number of valid, distinct alignments found for each read (M+1 actually). And reports only 1, the...
Forum: Bioinformatics 04-17-2012, 06:18 PM
Replies: 9
Views: 3,092
Posted By amaer
Awesome, thanks!

Awesome, thanks!
Forum: Bioinformatics 04-17-2012, 05:54 PM
Replies: 9
Views: 3,092
Posted By amaer
Thanks Jeremy for your very prompt reply. I was...

Thanks Jeremy for your very prompt reply. I was thinking too that varscan might do what I wanted, but upon reading the paper of VarScan2, it seemed that you would need at least 8% of all reads to be...
Forum: Bioinformatics 04-17-2012, 05:29 PM
Replies: 9
Views: 3,092
Posted By amaer
I am in a similar spot, Jeremy, have you figured...

I am in a similar spot, Jeremy, have you figured out anything?
Did you try software that call somatic mutations like SNVmix, varScan, SomaticSniper?
Forum: Metagenomics 03-26-2012, 08:21 AM
Replies: 3
Views: 2,658
Posted By amaer
Hello, Currently we are not handling...

Hello,

Currently we are not handling directly SOLiD data, but if we convert the reads from color space to plain nucleotide (A,C,G,T, etc.) sequences the pipeline should be able to handle it. We...
Forum: Metagenomics 03-15-2011, 01:39 PM
Replies: 3
Views: 2,658
Posted By amaer
Rapid Identification of Microorganisms in Solexa samples

My company (ICx Biosystems) has developed a Rapid Analysis Pipeline for Identification of bacteria and viruses in Solexa reads samples (RAPID). The software is ultra-fast and much more accurate than...
Forum: Bioinformatics 01-28-2010, 10:04 AM
Replies: 513
Views: 198,824
Posted By amaer
Hi Ben, What's the status of doing gapped...

Hi Ben,

What's the status of doing gapped alignments? Do you have an estimated date?

thanks, and keep up the great work!
Forum: Bioinformatics 11-16-2009, 09:54 PM
Replies: 513
Views: 198,824
Posted By amaer
concise mode and speed

Thanks a lot, Ben, that's very helpful. I have noticed that in my case running in the --concise mode is MUCH faster than the full mode (more than twice as fast). I don't mind using indexes instead...
Forum: Bioinformatics 11-12-2009, 01:37 PM
Replies: 513
Views: 198,824
Posted By amaer
eliminating redundancy from the output

Thanks, Ben, I would have liked to have the option of reading a zipped/gzipped file since that's how we receive the data from Solexa sequencing provider. Besides, the FASTQ files are quite big, and...
Forum: Bioinformatics 11-11-2009, 04:07 PM
Replies: 513
Views: 198,824
Posted By amaer
Gzipped files?

Hi Ben, Thanks for the update. Do you have an estimate about when Bowtie would be able to handle gzipped files for input and output?

Thanks,
Andreia
Forum: Bioinformatics 10-26-2009, 02:18 PM
Replies: 513
Views: 198,824
Posted By amaer
Hi Ben, What is the update on Bowtie doing...

Hi Ben,

What is the update on Bowtie doing gapped alignments?

Thanks!
Forum: Bioinformatics 10-26-2009, 01:55 PM
Replies: 22
Views: 34,326
Posted By amaer
Does SOAP2 perform gapped alignments yet?

Does SOAP2 perform gapped alignments yet?
Forum: Bioinformatics 10-26-2009, 01:50 PM
Replies: 0
Views: 3,527
Posted By amaer
SOAP2 and gapped alignments

Has anybody used SOAP2 with gapped alignments? If yes, what did you specify in parameters?

We recently got a Linux box and installed SOAP2 on it, the purpose of that being to do gapped alignments...
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