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Forum: Bioinformatics 03-30-2017, 08:01 PM
Replies: 24
Views: 9,784
Posted By keo
Hi all, This worked for me, but I don't know if...

Hi all,
This worked for me, but I don't know if it is a general solution. If you set the -k paramenter in Bowtie2 to >=2, you should have at least twice the name of the read in your SAM file. You...
Forum: Bioinformatics 01-17-2013, 04:11 PM
Replies: 2
Views: 1,837
Posted By keo
Hello Lluc, Perhaps you've resolved your...

Hello Lluc,
Perhaps you've resolved your questions by now, but I'll just post my answer anyway, and hope someone adds or corrects me.
I have had the same problem, and I haven't found a really "for...
Forum: Bioinformatics 02-08-2012, 12:13 PM
Replies: 5
Views: 2,605
Posted By keo
Hi, Thank you all for your suggestions, I'll...

Hi,
Thank you all for your suggestions, I'll try in the samtools mailing list. Just some pointers about the problem:
The bam files do open in IGV with no problem, and do show the deletions in the...
Forum: Bioinformatics 02-07-2012, 04:43 PM
Replies: 5
Views: 2,605
Posted By keo
Does bcftools generate valid VCF files?

Hello,
I am working with the output from a bcftools -cgA command, and it seems to be different from the VCF specification.
In particular it seems to show in some positions in the gene a REF as a...
Forum: General 02-02-2012, 07:23 AM
Replies: 4
Views: 3,970
Posted By keo
Thanks Jim, I'll keep this in mind. Best, ...

Thanks Jim,
I'll keep this in mind.
Best,
Keo.
Forum: General 02-01-2012, 06:04 AM
Replies: 4
Views: 3,970
Posted By keo
Hi all, Problem fixed. The IGV help team...

Hi all,
Problem fixed.
The IGV help team mentioned that the problem might be the reference, and I realized that my .genome file was built on the 32bit Vista machine. I just rebuilt the .genome file...
Forum: General 01-31-2012, 04:23 PM
Replies: 4
Views: 3,970
Posted By keo
Problems with display in IGV

Hello everybody,
I hope this is not off topic, I'm new in this forum.
I have installed IGV 2.0.34 on two Windows computers, one 32bit Vista
and another Windows7 64bit with graphics accelerator....
Forum: Introductions 01-26-2012, 06:17 PM
Replies: 0
Views: 819
Posted By keo
Hello from Mexico

Hello, I'm Keo,
I work as a staff Scientist in Mexico City, and trying to make the jump from cellular physiology to NGS (hint: it ain't easy!).
Best.
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