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Search: Posts Made By: donquijotes
Forum: Bioinformatics 06-28-2016, 10:06 AM
Replies: 5
Views: 1,856
Posted By donquijotes
HESmith, That was a fantastic paper, thank you...

HESmith, That was a fantastic paper, thank you for sharing!
Forum: Bioinformatics 06-20-2016, 07:55 AM
Replies: 5
Views: 1,856
Posted By donquijotes
Thank you sklages! It looks that people update...

Thank you sklages! It looks that people update these files frequently so the databases should be way better than the 2010 version the 1000genomes pilot study offers.
Forum: Bioinformatics 06-16-2016, 09:57 AM
Replies: 5
Views: 1,856
Posted By donquijotes
I've actually found this thread that might help. ...

I've actually found this thread that might help.

http://seqanswers.com/forums/showthread.php?t=23093
Two files that I found useful:
...
Forum: Bioinformatics 06-16-2016, 09:34 AM
Replies: 5
Views: 1,856
Posted By donquijotes
dbSNP database for just NA12878

So I may be completely wrong here but please correct me since I'm mostly used to doing RNA splicing analysis.

I have sequenced sheared DNA from about 10 NA12878 cells using Illumina and a library...
Forum: Bioinformatics 07-30-2015, 07:01 AM
Replies: 12
Views: 7,371
Posted By donquijotes
Help with UMI (unique molecular identifiers) data processing

I've been browsing different papers and publications and trying to figure out what's the best way to analyze data with UMIs.
So far I have used GATK to do some analysis couple of times, but other...
Forum: Bioinformatics 07-30-2015, 06:46 AM
Replies: 5
Views: 4,332
Posted By donquijotes
Hi nucacidhunter, Thank you for your input....

Hi nucacidhunter,

Thank you for your input. What I've seen many people do out there is read the UMI as part of their DNA library insert and not as part of the index. I still don't know how Agilent...
Forum: Bioinformatics 07-28-2015, 09:02 AM
Replies: 5
Views: 4,332
Posted By donquijotes
Hi sudders, From my very limited experience...

Hi sudders,

From my very limited experience with random barcodes, I've heard that this bias could be due to 2 reasons.
a) Synthesis bias. Some oligo companies suggest manually mixing the 4 bases...
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