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Forum: Academic/Non-Profit Jobs 06-22-2018, 06:12 AM
Replies: 0
Views: 586
Posted By turnersd
Bioinformatics analyst at the University of Virginia

Visit http://jobs.virginia.edu/applicants/Central?quickFind=83906 to apply.

The Bioinformatics Core in the UVa School of Medicine seeks a Bioinformatics Analyst. The analyst will work closely with...
Forum: Bioinformatics 11-25-2015, 04:05 AM
Replies: 5
Views: 2,460
Posted By turnersd
Brian - thanks for parsing Illumina's PDF and...

Brian - thanks for parsing Illumina's PDF and making the adapters available. It looks like as of Nov 9 2015 Illumina updated their adapter sequence document. Are there any notable changes that aren't...
Forum: Bioinformatics 10-28-2015, 04:30 AM
Replies: 4
Views: 718
Posted By turnersd
You might try the protocol. Maybe do a little...

You might try the protocol. Maybe do a little searching around before posting.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2952100/
Forum: Bioinformatics 10-12-2015, 04:27 AM
Replies: 13
Views: 1,398
Posted By turnersd
This may help. ...

This may help.

http://appris.bioinfo.cnio.es/

{APPRIS}
Annotating principal splice isoforms
Forum: Bioinformatics 09-21-2015, 06:32 AM
Replies: 67
Views: 18,228
Posted By turnersd
hey, what ever happened to the --paired option?...

hey, what ever happened to the --paired option? Is it still possible to screen paired end data?
Forum: Bioinformatics 02-17-2015, 01:25 AM
Replies: 7
Views: 5,783
Posted By turnersd
(Old post, but folks are still watching, still...

(Old post, but folks are still watching, still high google rank.)
Forum: RNA Sequencing 08-13-2014, 10:07 AM
Replies: 6
Views: 2,318
Posted By turnersd
Thanks for the helpful explanation, Brian.

Thanks for the helpful explanation, Brian.
Forum: RNA Sequencing 08-13-2014, 04:17 AM
Replies: 6
Views: 2,318
Posted By turnersd
Don't mean to side-track this discussion too...

Don't mean to side-track this discussion too much, but I'm noticing I have very poor coverage of a relatively small transcript (1200bp) after rRNA reduction and 2x100 sequencing, need to check on...
Forum: Bioinformatics 08-11-2014, 05:44 AM
Replies: 3
Views: 1,925
Posted By turnersd
Hey Mike. Thanks for responding. I'm working with...

Hey Mike. Thanks for responding. I'm working with Alex on this. We also used the plotPCA function and got the same results (the code used here to make the PCA plots was based on plotPCA - we had...
Forum: Bioinformatics 10-28-2013, 02:05 AM
Replies: 2
Views: 1,061
Posted By turnersd
The Galaxy Tool Shed might be helpful to see what...

The Galaxy Tool Shed might be helpful to see what people are actively using/developing.
Forum: Bioinformatics 07-09-2013, 12:32 PM
Replies: 2
Views: 9,500
Posted By turnersd
No paper that I've seen. See...

No paper that I've seen. See https://github.com/taoliu/MACS/
Forum: Bioinformatics 07-03-2013, 08:22 AM
Replies: 3
Views: 1,433
Posted By turnersd
Find binding sites for transcription factor in a sequence

I want to look at the promoter sequence of human IgM (ENSG00000162897 (http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000162897)), which I can easily retrieve with biomart. I'm specifically...
Forum: Bioinformatics 06-05-2013, 05:39 AM
Replies: 7
Views: 1,721
Posted By turnersd
I've used MACS and ZINBA on MEDIPS data, but this...

I've used MACS and ZINBA on MEDIPS data, but this data doesn't really look "peaky" the way other xIP experiments might, and not sure how methods like these that were mainly designed for ChIP-seq are...
Forum: Bioinformatics 06-05-2013, 05:12 AM
Replies: 7
Views: 1,721
Posted By turnersd
Haven't used SeqMonk. Take a look at MEDIPS...

Haven't used SeqMonk. Take a look at MEDIPS (http://www.bioconductor.org/packages/2.12/bioc/html/MEDIPS.html). What are others using for MeDIP-Seq analysis with biological replicates?
Forum: Bioinformatics 05-20-2013, 02:04 PM
Replies: 3
Views: 1,565
Posted By turnersd
I might consider making this an element in your...

I might consider making this an element in your design table, as was done with the pasilla library type variable in the DESeq vignette. But I'm not sure how necessary. Perhaps others can share their...
Forum: Bioinformatics 05-17-2013, 04:28 AM
Replies: 6
Views: 984
Posted By turnersd
Consider editing your title (if possible) to make...

Consider editing your title (if possible) to make this thread more informative.
Forum: Bioinformatics 05-13-2013, 10:31 AM
Replies: 5
Views: 3,732
Posted By turnersd
DESeq Normalization Question

I'm sure this issue has come up before, but I couldn't find an appropriate thread or answer either here or on the Bioconductor mailing list.

What feature of the data or the distribution of counts...
Forum: Bioinformatics 04-12-2013, 04:36 AM
Replies: 4
Views: 1,933
Posted By turnersd
I've used HTseq-count...

I've used HTseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html) to do this, but you could probably use bedtools as well. To use HTSeq I had to do some awk'ing of the BED file to...
Forum: Bioinformatics 03-13-2013, 10:38 AM
Replies: 123
Views: 40,919
Posted By turnersd
Great news, thanks Simon, Mike, Wolfgang. Looking...

Great news, thanks Simon, Mike, Wolfgang. Looking forward to going through the vignette. Are you publishing any comparisons with the original DESeq and/or other tools?
Forum: Bioinformatics 03-05-2013, 07:35 AM
Replies: 1
Views: 1,359
Posted By turnersd
Perhaps not the most accessible description, but...

Perhaps not the most accessible description, but this is from the official documentation:

http://cufflinks.cbcb.umd.edu/howitworks.html#hdif
Forum: Bioinformatics 02-21-2013, 04:24 AM
Replies: 9
Views: 3,573
Posted By turnersd
Bob (is that you Settlage?) - I'd love to see...

Bob (is that you Settlage?) - I'd love to see what you think if you try both approaches.
Forum: Bioinformatics 02-19-2013, 08:21 AM
Replies: 2
Views: 867
Posted By turnersd
http://sourceforge.net/projects/biogrinder/

http://sourceforge.net/projects/biogrinder/
Forum: Bioinformatics 02-19-2013, 06:37 AM
Replies: 3
Views: 1,892
Posted By turnersd
I'm sure there are others here but that was one...

I'm sure there are others here but that was one of the most recent.
Forum: Bioinformatics 02-19-2013, 06:29 AM
Replies: 3
Views: 1,892
Posted By turnersd
http://seqanswers.com/forums/showthread.php?t=2604...

http://seqanswers.com/forums/showthread.php?t=26043
Forum: Bioinformatics 02-14-2013, 04:43 PM
Replies: 9
Views: 3,573
Posted By turnersd
Thanks dstorey. I also recently came across this...

Thanks dstorey. I also recently came across this method for partitioning reads to their respective species before mapping. Might give it a try.

http://www.ncbi.nlm.nih.gov/pubmed/22689758
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