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Search: Posts Made By: Soni
Forum: Bioinformatics 12-17-2013, 11:04 PM
Replies: 6
Views: 2,813
Posted By Soni
Thanks tospo. It worked through the commandline.

Thanks tospo. It worked through the commandline.
Forum: Bioinformatics 12-11-2013, 05:15 AM
Replies: 6
Views: 2,813
Posted By Soni
Hi topso. Yes I can load both the files (see...

Hi topso.
Yes I can load both the files (see screenshot 1 below).
When I clone the window and select a different bam file to appear in each window I get screenshot 2.
:confused:
Cheers
Forum: Bioinformatics 12-11-2013, 12:09 AM
Replies: 6
Views: 2,813
Posted By Soni
Thanks for posting this tospo. I tried it...

Thanks for posting this tospo.

I tried it but it's still not working. The second .bam file I load doesn't appear in the cloned window. Only the first one does. I tried several views too but with...
Forum: Bioinformatics 12-06-2011, 09:58 PM
Replies: 2
Views: 1,900
Posted By Soni
Thanks for your reply vamosia. That is exactly...

Thanks for your reply vamosia. That is exactly why it is baffling me as those SVs have 'High' confidence and are in the 454HCStructVars.txt.
Forum: Bioinformatics 12-06-2011, 04:08 AM
Replies: 2
Views: 1,900
Posted By Soni
Structural variations using Newbler mapper

Hi,

Would anyone know how gsMapper decides on a consensus especially over a region that has structural variations? I am looking in 454HCStructVars.txt and 454HCStructRearrangements.txt to identify...
Forum: Bioinformatics 06-14-2011, 11:36 PM
Replies: 1
Views: 1,595
Posted By Soni
Hi, You can parse the headers of the...

Hi,
You can parse the headers of the 454AllContigs.fna to get the start and stop coordinates of the reference mapped by that particular contig. By a simple loop to substract the latter start...
Forum: De novo discovery 06-09-2011, 03:58 AM
Replies: 12
Views: 9,265
Posted By Soni
Greigite, How did you get on with MIRA? Is...

Greigite,

How did you get on with MIRA? Is handling SNPs easier with that? I've never used MIRA and am doing a lot of SNP identification so I will be very interested to hear your views.

Cheers.
Forum: De novo discovery 06-09-2011, 03:55 AM
Replies: 12
Views: 9,265
Posted By Soni
Hi hlu, Thank you very much for providing me...

Hi hlu,
Thank you very much for providing me with an explanation on why the SNP positions in the 454AlignmentInfo.tsv appear as they do when compared with 454HCDiffs.txt.

Would you know of an...
Forum: Bioinformatics 08-19-2010, 07:10 AM
Replies: 19
Views: 6,526
Posted By Soni
Thanks for your quick reply adamdeluca. But does...

Thanks for your quick reply adamdeluca. But does this mean gsMapper reads base 0 as the 1st base or do I have to add the base anyway (cos I've done the latter).

If I don't then you might have...
Forum: Bioinformatics 08-19-2010, 06:53 AM
Replies: 19
Views: 6,526
Posted By Soni
I have a related question. I am trying to...

I have a related question.

I am trying to identify SNPs using gsMapper. I have an annotated reference genome and since my genome is not in USCS I've had to convert the format from gb to refGene...
Forum: 454 Pyrosequencing 10-16-2009, 07:51 AM
Replies: 11
Views: 6,666
Posted By Soni
Newbler manual

Does anyone have a copy of the newbler/GS de novo assembler software user manual? I can't find one on the internet...Cheers.
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