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Forum: Epigenetics 09-14-2011, 11:12 AM
Replies: 8
Views: 6,058
Posted By JohnK@Genome_Quest
Large duplication in SE ChIP-Seq libraries is a...

Large duplication in SE ChIP-Seq libraries is a typical result of PCR. This can directly reflect the difficulty in isolating your protein via cross-linkers or how effective your antibodies are. ...
Forum: Bioinformatics 07-29-2011, 12:09 PM
Replies: 2
Views: 1,591
Posted By JohnK@Genome_Quest
Call your SNPs, get your junction locations, and...

Call your SNPs, get your junction locations, and then filter your SNPs.
Forum: Bioinformatics 06-07-2011, 01:38 PM
Replies: 3
Views: 2,338
Posted By JohnK@Genome_Quest
If you're experimentally verifying the real...

If you're experimentally verifying the real patterns, I imagine you could confirm your True Positives by comparing them to your experimentally-validated pattern data. As for your False Positives,...
Forum: Bioinformatics 06-07-2011, 01:29 PM
Replies: 3
Views: 3,364
Posted By JohnK@Genome_Quest
You could try to download liftOver program binary...

You could try to download liftOver program binary from the Kent Source Tree @ UCSC.
Forum: Bioinformatics 06-07-2011, 01:27 PM
Replies: 5
Views: 5,674
Posted By JohnK@Genome_Quest
Maybe their servers are down. The full command...

Maybe their servers are down. The full command didn't work for me, but what you can do is go type:

ftp ftp.ncbi.nih.gov

, And then just follow the path to the directory you specified by:

...
Forum: Bioinformatics 06-06-2011, 08:51 PM
Replies: 15
Views: 9,564
Posted By JohnK@Genome_Quest
I used to use Cygwin when I used Windows. Once...

I used to use Cygwin when I used Windows. Once you figure out how Cygwin's files are setup and tied in to Windows, which should be fairly easy to figure out, you can figure out how to navigate to...
Forum: Bioinformatics 06-06-2011, 08:47 PM
Replies: 8
Views: 3,882
Posted By JohnK@Genome_Quest
One read is kept.

One read is kept.
Forum: Bioinformatics 06-06-2011, 11:45 AM
Replies: 8
Views: 3,882
Posted By JohnK@Genome_Quest
Also, I removed PCR duplicates for all...

Also, I removed PCR duplicates for all applications- even RNA-Seq. Clearly, if you're trying to estimate transcript abundance, or estimate splicing-efficiency then PCR duplicates will have some sort...
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