Forum: Academic/Non-Profit Jobs
08-28-2018, 08:47 AM
|
|
Replies: 0
Views: 1,173
WASHU Postdoctoral Research Associate
WASHU Postdoctoral Research Associate - Pediatrics Hematology/Oncology
https://www.indeed.com/viewjob?jk=55f2d6daf5426994&tk=1clooucmc185b4h3&from=serp&vjs=3
This position is in the Department...
|
|
Forum: General
07-09-2017, 04:36 PM
|
|
Replies: 10
Views: 14,274
I'm not sure I follow. It doesn't...
I'm not sure I follow. It doesn't reverse-complement the "regular expression" it reverse complements the restriction enzyme sequence (a string) that is used in the regular expression. We can either...
|
|
Forum: Bioinformatics
10-14-2013, 04:24 PM
|
|
Replies: 0
Views: 1,932
DGIdb: Mining the Druggable Genome
The druggable genome can be defined as the genes or gene products that are known or predicted to interact with drugs, ideally with a therapeutic benefit to patients. We developed the Drug Gene...
|
|
Forum: Bioinformatics
01-09-2013, 09:07 AM
|
|
Replies: 15
Views: 9,294
It looks like nilshomer's initial question was...
It looks like nilshomer's initial question was never addressed. We have the same concern with using this software:
"Looks like the license is fairly restrictive. Any chance of moving this to an...
|
|
Forum: Bioinformatics
12-07-2011, 08:38 AM
|
|
Replies: 13
Views: 12,150
|
|
Forum: Bioinformatics
09-15-2011, 11:46 AM
|
|
Replies: 19
Views: 13,710
The ALEXA-seq...
The ALEXA-seq (http://www.ncbi.nlm.nih.gov/pubmed/20835245) and Trans-ABySS (http://www.ncbi.nlm.nih.gov/pubmed/20935650) manuscripts discuss the implications of intronic mapping reads for measuring...
|
|
Forum: RNA Sequencing
09-14-2011, 09:18 AM
|
|
Replies: 3
Views: 4,332
|
|
Forum: Bioinformatics
08-16-2011, 06:56 AM
|
|
Replies: 5
Views: 5,180
kmcarr makes some good suggestions.
More...
kmcarr makes some good suggestions.
More options:
Splign (http://www.ncbi.nlm.nih.gov/sutils/splign/splign.cgi)
Spidey (http://www.ncbi.nlm.nih.gov/spidey/)
If you look at a Refseq record...
|
|
Forum: Bioinformatics
06-27-2011, 05:13 PM
|
|
Replies: 30
Views: 12,379
I would also suggest you update to 0.4.2. The...
I would also suggest you update to 0.4.2. The way these things are specified in the config file have changed slightly. The new example may be more clear. After you have tried that, if you are...
|
|
Forum: Introductions
05-19-2011, 09:24 PM
|
|
Replies: 2
Views: 2,044
|
|
Forum: Bioinformatics
05-19-2011, 08:07 PM
|
|
Replies: 13
Views: 12,150
Tools for detecting alternative splicing events
In addition to MISO and Cufflinks, ALEXA-seq (http://www.alexaplatform.org/alexa_seq/) is another tool that focuses on analysis at the feature level (exon, exon-exon junction, intron, etc.). The...
|
|
Forum: Bioinformatics
11-19-2010, 12:17 PM
|
|
Replies: 9
Views: 2,042
Regarding the comment that the observation may...
Regarding the comment that the observation may simply be due to biology. Good point! Once you convince yourself that the observation is not due to an artifact of the analysis (mapability, small...
|
|
Forum: Bioinformatics
11-19-2010, 11:41 AM
|
|
Replies: 9
Views: 2,042
|
|
Forum: RNA Sequencing
11-18-2010, 12:13 AM
|
|
Replies: 23
Views: 10,242
Yeah, I would agree with that. It really...
Yeah, I would agree with that. It really invaluable to have a few decent boxes (high memory ones even better) that have access to all the same storage mounts as the cluster nodes themselves...
|
|
Forum: RNA Sequencing
11-17-2010, 03:15 PM
|
|
Replies: 23
Views: 10,242
|
|
Forum: General
11-17-2010, 03:00 PM
|
|
Replies: 10
Views: 14,274
In case you feel that my previous post was...
In case you feel that my previous post was dodging your question :) ... attached is an example Perl script that you could use as a starting point. It uses regex to identify occurrences of one...
|
|
Forum: General
11-17-2010, 02:19 PM
|
|
Replies: 10
Views: 14,274
This should be fun. A real classic...
This should be fun. A real classic bioinformatics task for beginners.
There are some good books out there for learning how to solve these problems.
Beginning Perl for Bioinformatics...
|
|
Forum: Bioinformatics
11-17-2010, 12:53 PM
|
|
Replies: 9
Views: 2,042
|
|
Forum: RNA Sequencing
11-17-2010, 12:39 PM
|
|
Replies: 23
Views: 10,242
Our cluster uses Sun Grid Engine (sge). ...
Our cluster uses Sun Grid Engine (sge). Submitting jobs to the cluster is accomplished using a wrapper for the 'qsub' utility of sge. Basically the submission command is just pointing to a batch...
|
|
Forum: Bioinformatics
11-16-2010, 10:22 PM
|
|
Replies: 5
Views: 5,695
Hello hanifk,
Welcome to the wonderful...
Hello hanifk,
Welcome to the wonderful world of RNA-seq analysis. :).
RNA-seq can have very good signal-to-noise ratios compared to other expression analysis methods (e.g. microarrays). ...
|
|
Forum: RNA Sequencing
11-16-2010, 05:52 PM
|
|
Replies: 6
Views: 9,378
|
|
Forum: General
11-16-2010, 05:08 PM
|
|
Replies: 10
Views: 8,126
|
|
Forum: Bioinformatics
11-16-2010, 02:20 AM
|
|
Replies: 3
Views: 1,890
It seems like the next-gen, fast, short read...
It seems like the next-gen, fast, short read aligners are generally focused on aligning entire reads and do not do substring alignments. You may be stuck using an old school aligner. BLAST...
|
|
Forum: Bioinformatics
11-16-2010, 02:03 AM
|
|
Replies: 7
Views: 4,066
I believe assembled size includes the size of...
I believe assembled size includes the size of known gaps in the genome assembly. The sequenced size does not include the size of these gaps. Using physical mapping of a genome (e.g. BAC library...
|
|
Forum: Bioinformatics
11-16-2010, 01:40 AM
|
|
Replies: 3
Views: 2,354
|
