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Forum: Literature Watch 10-20-2015, 02:13 AM
Replies: 46
Views: 44,023
Posted By jflores
Hello Alicia, The most straight forward...

Hello Alicia,

The most straight forward design you can employ here is to simply choose one of your test#.hits files as the reference. You can use the sample with the highest coverage as...
Forum: Literature Watch 07-09-2011, 11:36 AM
Replies: 46
Views: 44,023
Posted By jflores
Hi Tonio, You can plot specific coordinates...

Hi Tonio,

You can plot specific coordinates and try to infer from that if your gene of interest has or not gain/loss of copies.

Script :
samtools view...
Forum: Literature Watch 04-28-2011, 11:37 PM
Replies: 46
Views: 44,023
Posted By jflores
Hi Sergio, With CNV-seq in mind and for...

Hi Sergio,

With CNV-seq in mind and for non-control-case studies you can basically choose whatever reference you want. There might be some issues to worry about like what population the reference...
Forum: Literature Watch 04-28-2011, 11:24 PM
Replies: 46
Views: 44,023
Posted By jflores
Hi Louis, CNV-seq input consists in just...

Hi Louis,

CNV-seq input consists in just two files (reference & test) with just two columns each.
First column corresponds to the third column in a BAM file, that is the reference sequence name...
Forum: Bioinformatics 04-28-2011, 05:01 PM
Replies: 3
Views: 5,118
Posted By jflores
Hi Jason, Cheers for the response ! I'm...

Hi Jason,

Cheers for the response ! I'm interested just in one chromosome so I'm e-mailing you right now,
Forum: Bioinformatics 04-28-2011, 04:38 PM
Replies: 3
Views: 5,118
Posted By jflores
Conversion from Complete Genomics Data to SAM/BAM

Hi There !

This thread is intended to questions related to conversion from Complete Genomics Data to SAM/BAM formats.

So here's mine:

I'm trying to get BAM files for some of the individuals...
Forum: Bioinformatics 03-30-2011, 05:05 PM
Replies: 3
Views: 9,049
Posted By jflores
Hi dnusol, Very delayed response, hopefully...

Hi dnusol,

Very delayed response, hopefully you not only know the answer but can help me a bit.

Underline: secondary or orphan ---what is this?
Blue: 0-9 --- 0-9 what? is it number of reads?...
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