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Forum: Introductions 07-22-2010, 10:21 PM
Replies: 373
Views: 179,410
Posted By AvinashP
Hi to all

hi,

I am a software engineer who was exposed to bioinformatics and sequencing two years back. Since then, i have been hooked on to this field. I have worked on Illumina short reads. Working on...
Forum: Bioinformatics 06-28-2010, 01:16 AM
Replies: 2
Views: 3,348
Posted By AvinashP
Thanks, but i faced difficulty finding the...

Thanks,
but i faced difficulty finding the right answers.
Can you please point me to any links giving the answers ?

Thanks
Forum: Bioinformatics 06-24-2010, 06:10 AM
Replies: 2
Views: 3,348
Posted By AvinashP
Samtools Merge and rmdup

hi,

I have 7 bam files which i need to merge into a single one.

1. Should i first sort the bam files and then merge or merge it first and then sort ?
2. Is it important to do a 'rmpup' ? Does...
Forum: Bioinformatics 06-11-2010, 01:12 AM
Replies: 2
Views: 5,103
Posted By AvinashP
Input to BWA from multiple Lanes

hi,

I have paired end data from multiple lanes (illumina pipleine) in qseq format.
i convert all the qseq files to fastq lane wise.
Combine the first sequences in one file and the next...
Forum: Genomic Resequencing 06-08-2010, 03:11 AM
Replies: 2
Views: 5,562
Posted By AvinashP
Thanks, for your immediate reply. For (2.)...

Thanks, for your immediate reply.

For (2.) can we restrict the indels with the parameters -o and -e in the 'aln' step? What is the ideal value for these parameters given 115bp reads ?

4. i want...
Forum: Genomic Resequencing 06-07-2010, 03:39 AM
Replies: 2
Views: 5,562
Posted By AvinashP
BWA alignment for paired end reads

hi,

i am using BWA to align 115bp paired end solexa reads. I have the following doubts :-

1. Does BWA take the min and max insert sizes for paired end reads ?
2. What is maximum number of...
Forum: Introductions 06-07-2010, 03:18 AM
Replies: 0
Views: 1,062
Posted By AvinashP
Smile Hi All

Hi all,

i am a new user and working on Solexa reads.
I am interested in working on various Bioinformatics Tools especially related to alignment.
Hope to gain a lot of help from all the...
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