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Search: Posts Made By: sandhya
Forum: Bioinformatics 09-01-2011, 05:29 AM
Replies: 1
Views: 2,100
Posted By sandhya
Errors encountered while running Metasim

Hi,

I am using Metasim to simulate 454 reads. This is the 454 error model setting.

The Taxon profile is


I run into this error (this is from the Simulator log file)
Forum: Bioinformatics 10-25-2010, 05:25 AM
Replies: 11
Views: 3,033
Posted By sandhya
Thank you all for the comments and replies. I do...

Thank you all for the comments and replies. I do agree that one has to resort to trickery when it comes to processing huge files no matter which language one uses. I also checked 'seqan' but they do...
Forum: Bioinformatics 10-19-2010, 09:45 AM
Replies: 11
Views: 3,033
Posted By sandhya
The reason I asked for C++ was because I work...

The reason I asked for C++ was because I work with it. C should also be alright.
I shall have a look at (http://lh3lh3.users.sourceforge.net/parsefastq.shtm) in detail but on first-hand I...
Forum: Bioinformatics 10-19-2010, 05:44 AM
Replies: 11
Views: 3,033
Posted By sandhya
C++ library for bioinformatics?

Hi,

This is a software related question and I am hoping someone in this forum could throw light in this direction. We work on mathematical analyses with FASTA and FASTQ files. So far we have...
Forum: Bioinformatics 09-15-2010, 06:33 AM
Replies: 0
Views: 1,404
Posted By sandhya
Novoalign native report - Paired reads

Hi,

If anyone has worked with a report (native format) generated using novoalign, please help me with these doubts. The datasets used are Illumina paired reads.

A) Below is the snapshot of a...
Forum: Bioinformatics 09-15-2010, 02:48 AM
Replies: 1
Views: 2,036
Posted By sandhya
Posting the reply from Novocraft's forum for this...

Posting the reply from Novocraft's forum for this thread from zayed
**********
On Tue 14 of Sep., 2010 12:48 MYT, by zayed
OK, it looks as though you may not have built your database index before...
Forum: Bioinformatics 09-13-2010, 01:50 AM
Replies: 10
Views: 12,411
Posted By sandhya
Oh I see. Thank you for forewarning me about...

Oh I see. Thank you for forewarning me about that. I shall keep this in mind and see if there is a workaround for it in R.
Forum: Bioinformatics 09-13-2010, 12:40 AM
Replies: 10
Views: 12,411
Posted By sandhya
I understand the sentences separately but when I...

I understand the sentences separately but when I read them together I find them contradictory. Please let me know about any reading material to familiarise with these concepts. Again what does 'main...
Forum: Bioinformatics 09-10-2010, 07:13 AM
Replies: 1
Views: 2,036
Posted By sandhya
Novoalign error message:- Interrupted..11 Obtained 7 stack frames.

Hi,

I receive the following error while aligning paired-end reads using novoalign.

Interrupted..11
Obtained 7 stack frames.
0x400348
0x4003cd
0x43d860
0x40df50
Forum: Bioinformatics 09-10-2010, 05:18 AM
Replies: 10
Views: 12,411
Posted By sandhya
Thank you, maubp for the reply. In the wiki it is...

Thank you, maubp for the reply. In the wiki it is mentioned that Illumina uses a /1 or /2 suffix. Are there cases when the suffix is not present or does this mean these are not Illumina-generated...
Forum: Bioinformatics 09-09-2010, 11:50 PM
Replies: 10
Views: 12,411
Posted By sandhya
Fastq format and Paired-end reads

Dear all,

I have recently started work on sequenced data. We have paired-end reads from Illumina in Fastq format and I had some questions about these.

1. In the fastq format, what do the...
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