Forum: Bioinformatics
08-25-2011, 04:43 PM
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Replies: 0
Views: 1,623
New company in the making. Need team members.
Hi all,
I've set up a system with the intention of commercializing it in a few years. It's supported and guided by teachers at Copenhagen University, Dana Farber Cancer Institute (Harvard) and at...
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Forum: Bioinformatics
08-17-2011, 05:44 AM
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Replies: 13
Views: 5,958
A size file is just a file with chromosome name...
A size file is just a file with chromosome name and it's length. i've attached 2 text files. The chrom2 is the one you should probably use, the other has lengths of all hg19 chromosomes(alternative...
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Forum: Bioinformatics
08-10-2011, 02:10 AM
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Replies: 13
Views: 5,958
@ Upendra
Thanks a lot for the mail. It all...
@ Upendra
Thanks a lot for the mail. It all works well now.
I have one small question.
In the bed file there are some transcripts with a * instead of +/- for orientation. What does this mean?
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Forum: Bioinformatics
08-08-2011, 02:30 AM
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Replies: 13
Views: 5,958
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Forum: Bioinformatics
08-07-2011, 02:49 PM
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Replies: 13
Views: 5,958
Hey,
That'd be awesome. My e-mail is...
Hey,
That'd be awesome. My e-mail is orsha.pk@gmail.com
I've tried the three versions of scripture they've put on the website, none of them have this older function. Maybe they should include...
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Forum: SOLiD
08-07-2011, 04:05 AM
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Replies: 5
Views: 4,080
Hi,
I looked at this tutorial and was...
Hi,
I looked at this tutorial and was looking for the "scripture_alpha2.jar" file. I cannot find that file anywhere. Any insights or help would be appreciated.
Thanks!
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Forum: RNA Sequencing
08-07-2011, 04:03 AM
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Replies: 1
Views: 1,588
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Forum: Bioinformatics
08-07-2011, 04:00 AM
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Replies: 1
Views: 1,372
Try using this...
perl -ne '@l = split;...
Try using this...
perl -ne '@l = split; $l[4]=1; print "@l[0..11]\n";' < chr1.bed > c.bed
I assume that this file is called chr1.bed.
The output will be stored in c.bed
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Forum: Bioinformatics
08-07-2011, 03:38 AM
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Replies: 13
Views: 5,958
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Forum: Bioinformatics
08-07-2011, 03:26 AM
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Replies: 13
Views: 5,958
Hi,
Thanks for the reply.
I have 2...
Hi,
Thanks for the reply.
I have 2 questions on this link...
1. In the IGVtools count command, what is the .genome file? Rather how do you get it? I tried the .fa reference genome but that...
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Forum: Bioinformatics
08-06-2011, 07:19 AM
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Replies: 13
Views: 5,958
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Forum: Bioinformatics
04-11-2011, 04:43 AM
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Replies: 11
Views: 11,070
Field MAPQ considers pairing in calculation if...
Field MAPQ considers pairing in calculation if the read is paired. If such a calculation is difficult, 255 is applied, indicating the mapping quality is not available. I assume your query sequences...
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Forum: Bioinformatics
04-11-2011, 04:35 AM
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Replies: 2
Views: 1,552
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Forum: Bioinformatics
04-10-2011, 09:44 PM
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Replies: 2
Views: 1,552
Need your views on a custom pipeline
Hi,
Here's a link to my most recent presentations. My team created a pipeline to map sequences to a custom dataset using the BWA aligner. The pipeline also gives some stats and does an error...
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Forum: Genomic Resequencing
03-16-2011, 04:30 PM
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Replies: 7
Views: 5,111
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Forum: Genomic Resequencing
03-10-2011, 04:32 AM
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Replies: 7
Views: 5,111
My study involves divergence study on the gene...
My study involves divergence study on the gene p53 on short arm of chromosome 17. I need to extract this part of the sequence.
I understand that I can do this in two ways:
1. Get raw fasta reads....
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Forum: Genomic Resequencing
02-28-2011, 12:36 PM
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Replies: 7
Views: 5,111
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Forum: Introductions
02-28-2011, 07:31 AM
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Replies: 0
Views: 839
Hello!
Hi,
I'm Pranav and I'm from India. I'm doing my Masters in Bio-Informatics at the Copenhagen University in Denmark.
I'm currently working on a pipeline that uses BWA aligner to align an...
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Forum: Genomic Resequencing
02-28-2011, 07:20 AM
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Replies: 4
Views: 7,980
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Forum: Introductions
02-28-2011, 07:16 AM
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Replies: 33
Views: 9,183
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Forum: Genomic Resequencing
02-28-2011, 07:05 AM
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Replies: 7
Views: 5,111
Understanding BAM format.
Hi,
I have this output in BAM format.
(This is data from the 1000 genomics project.)
I'm constructing a pipeline to study variations (I get fast-q sequence, index it, align it to ref.seq...
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