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Forum: Bioinformatics 02-23-2012, 08:47 AM
Replies: 4
Views: 1,700
Posted By PratikC
Question Hi aurelielaugraud, Thanks for gem mapper. ...

Hi aurelielaugraud,

Thanks for gem mapper.
In gem mapper I need to specify at what length sequence to be splited.

Actually what I need is not to specify the sequence length to be mapped....
Forum: Bioinformatics 02-23-2012, 01:17 AM
Replies: 4
Views: 1,700
Posted By PratikC
Question Partial alignment of Illumina reads.

Hi all,
I have fastq files having Illumina paired end sequence reads. I want to align a part of read say read length is 75 bases and I want alignment in which at least 50 bases are aligned without...
Forum: Bioinformatics 01-16-2012, 09:59 AM
Replies: 2
Views: 1,319
Posted By PratikC
Hi Neha, Plz post your question in a new...

Hi Neha,
Plz post your question in a new thread...this thread is not for discussing Rocks related questions...
Forum: Bioinformatics 10-11-2011, 11:40 PM
Replies: 14
Views: 7,843
Posted By PratikC
Hi Husamia, yes its pooled sample and we are not...

Hi Husamia, yes its pooled sample and we are not demultiplexing before alignment. We just want to find out which mutation is there in population, we don't care which mutated gene coming from which...
Forum: Bioinformatics 10-11-2011, 11:33 PM
Replies: 14
Views: 7,843
Posted By PratikC
Thumbs up Cheers!!!

Thanks Heisman, I got your point and will do as you said.
Thank you very much.
Again, can you suggest any article of yours or others showing similar kind of custom reference in NGS analysis...
Forum: Bioinformatics 10-11-2011, 11:47 AM
Replies: 14
Views: 7,843
Posted By PratikC
Thumbs up Thanks Heisman, I got your point. I am doing that...

Thanks Heisman, I got your point. I am doing that part and going fine with it. My question was like when we do dbSNP annotation, if our seq is mapped to ref genome, program will annotate dbSNPs on...
Forum: Bioinformatics 10-11-2011, 12:30 AM
Replies: 14
Views: 7,843
Posted By PratikC
Smile Hi Heisman, I already started mpileup and hopes...

Hi Heisman, I already started mpileup and hopes it will be completed soon. Meanwhile, if possible, can you plz give me some more details of how you set up custom reference sequences and then how you...
Forum: Bioinformatics 10-09-2011, 01:23 PM
Replies: 14
Views: 7,843
Posted By PratikC
Sorry friends for late reply. Thnx aaronh and...

Sorry friends for late reply. Thnx aaronh and colindaven. Yes my seq read is of 18GB and only 3 genes are there, but keep in mind its pooled sequencing so we got around 25 samples. Now coming to the...
Forum: Bioinformatics 10-04-2011, 07:42 PM
Replies: 14
Views: 7,843
Posted By PratikC
Question mapping on to custom reference sequence

Hi,
I have sequence read data of 3 particular genes of Human.
I know their location on reference genome and so I retrieved their sequences and made another fasta file with regular header...
Forum: Bioinformatics 09-15-2011, 02:40 AM
Replies: 17
Views: 8,681
Posted By PratikC
Thank you very much GenoMax, the link you gave is...

Thank you very much GenoMax, the link you gave is very useful.
Forum: Bioinformatics 09-14-2011, 07:09 AM
Replies: 17
Views: 8,681
Posted By PratikC
Guys, what do you say about cloud computing? If...

Guys, what do you say about cloud computing? If anyone has experience of clouds, please suggest which one is better in terms of cost and processing? We have got 10 Mbps dedicated line and we are...
Forum: Bioinformatics 09-13-2011, 06:28 AM
Replies: 17
Views: 8,681
Posted By PratikC
Smile Thanks GenoMax. I checked rocks, its really...

Thanks GenoMax.
I checked rocks, its really very good. I will try it out ASAP!



Thanks zee,
as I said we are not doing whole genome analysis but exome and targeted sequencing and so I am...
Forum: Bioinformatics 09-12-2011, 10:09 AM
Replies: 17
Views: 8,681
Posted By PratikC
Thanks rskr and lh3. I understood the limitation...

Thanks rskr and lh3. I understood the limitation of GPU at this time, may be in near future there will be many other software ported to GPU but right now cluster is better.
I still dont understand...
Forum: Bioinformatics 09-12-2011, 06:57 AM
Replies: 17
Views: 8,681
Posted By PratikC
Thanx GenoMax and gprakhar. I understand that...

Thanx GenoMax and gprakhar.
I understand that GPU is not suitable for NGS data analysis at this point because no good software ported to GPU.
About cluster, what you people suggest is for network...
Forum: Bioinformatics 09-11-2011, 09:29 AM
Replies: 17
Views: 8,681
Posted By PratikC
I already checked that. But mummer and ugene are...

I already checked that. But mummer and ugene are ported to GPGPU and my question is not limited to GPU but a comparison like workstation/server having multi core processor and single/dual HDD will be...
Forum: Bioinformatics 09-10-2011, 12:57 AM
Replies: 17
Views: 8,681
Posted By PratikC
Question GPU/Cluster/Server based systems for NGS

Hi all,
I am new to NGS field but I do understand some of the things and now want to know about better hardware required for NGS data analysis.
Please explain with respect to categories
1) Whole...
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