Forum: Bioinformatics
08-23-2010, 03:09 AM
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Replies: 3
Views: 3,052
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Forum: Bioinformatics
08-23-2010, 02:13 AM
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Replies: 3
Views: 3,052
High throughput Gene Ontology enrichment API
A bioinformatics question: I have been doing more and more Gene Ontology (GO) work, specifically, I am looking for enriched terms in my various gene sets. I usually go through the web-based programs...
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Forum: RNA Sequencing
07-07-2009, 02:22 AM
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Replies: 9
Views: 12,401
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Forum: Illumina/Solexa
07-06-2009, 06:43 AM
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Replies: 3
Views: 2,168
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Forum: Illumina/Solexa
07-06-2009, 03:34 AM
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Replies: 3
Views: 2,168
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Forum: Academic/Non-Profit Jobs
06-26-2009, 05:24 AM
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Replies: 6
Views: 3,629
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Forum: Epigenetics
06-25-2009, 01:02 AM
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Replies: 13
Views: 8,147
40-60% using the default ELAND settings is a...
40-60% using the default ELAND settings is a little on the low side for 36bp (paired end?). If you want to try alternate settings, bowtie (see the forum here) is very amenable to messing around with...
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Forum: Academic/Non-Profit Jobs
06-22-2009, 02:19 AM
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Replies: 6
Views: 3,629
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Forum: Academic/Non-Profit Jobs
06-18-2009, 06:19 AM
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Replies: 6
Views: 3,629
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Forum: Academic/Non-Profit Jobs
06-18-2009, 02:14 AM
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Replies: 6
Views: 3,629
Looking for advice on european genomics
Hi All,
I am in the final year of my PhD and starting to get a little worried about what I am going to do next...:confused:
I don't think I want to do a postdoc, but I love what I do...
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Forum: Bioinformatics
06-16-2009, 08:03 AM
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Replies: 514
Views: 225,972
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Forum: Bioinformatics
06-16-2009, 05:02 AM
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Replies: 514
Views: 225,972
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Forum: Bioinformatics
06-15-2009, 10:30 AM
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Replies: 514
Views: 225,972
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Forum: Bioinformatics
06-15-2009, 10:18 AM
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Replies: 514
Views: 225,972
Hi Ben,
Quick question - if you supply...
Hi Ben,
Quick question - if you supply paired end arguments (--ff / -I / etc...) , but only supply a <singles> file (not <mates1/2>), will the PE args just be ignored?
Similarly, if I specify...
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Forum: Epigenetics
06-08-2009, 03:07 AM
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Replies: 20
Views: 76,124
might want to add PeakSeq too:
...
might want to add PeakSeq too:
http://www.nature.com/nbt/journal/v27/n1/full/nbt.1518.html
Not earth-shattering, but i think their advice on normalising to input is really worthwhile.
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Forum: RNA Sequencing
06-04-2009, 01:44 AM
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Replies: 36
Views: 27,790
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Forum: RNA Sequencing
06-04-2009, 01:41 AM
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Replies: 9
Views: 12,401
Hi all, We have had success with PE RNAseq...
Hi all, We have had success with PE RNAseq (illumina).
Some of the main pitfalls that we found:
-when you make your cDNA, if you use random hexamers (best results for us), your first strand...
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Forum: Bioinformatics
04-07-2009, 01:48 AM
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Replies: 514
Views: 225,972
Hi Ben,
I have seen this in 0.9.9 and...
Hi Ben,
I have seen this in 0.9.9 and 0.9.9.1 (x64), m.musculus ncbi36 and 37 indices (offrates 2,3,4,5). Args were -q --solexa-quals -a --unfq ... -p 2/3/6 . Input was only ~1/2 Mb of fastq...
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Forum: Bioinformatics
04-06-2009, 10:42 AM
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Replies: 514
Views: 225,972
Hi Ben,
Thanks for your advice earlier,...
Hi Ben,
Thanks for your advice earlier, post-processing of results is now working well!
However I have found that using --all isn't a problem, until i specify --nostrata as well which causes...
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Forum: Bioinformatics
03-13-2009, 05:59 AM
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Replies: 4
Views: 2,913
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Forum: Bioinformatics
03-13-2009, 05:51 AM
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Replies: 4
Views: 2,913
Hi,
A very good paper came out recently :...
Hi,
A very good paper came out recently : "PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls" Rozowsky et al Nat. Biotech. (2009) 27(1):66-
It answers a lot of...
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Forum: Bioinformatics
03-11-2009, 05:33 AM
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Replies: 514
Views: 225,972
Hi Ben,
Thanks for your help so far - I am...
Hi Ben,
Thanks for your help so far - I am relatively new to mapping (but not so new that I am not impressed by bowtie!), so please excuse any dopey questions...
My worry is that I will lose...
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Forum: Bioinformatics
03-10-2009, 10:48 AM
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Replies: 514
Views: 225,972
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Forum: Bioinformatics
03-10-2009, 08:35 AM
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Replies: 514
Views: 225,972
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Forum: Bioinformatics
03-10-2009, 07:35 AM
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Replies: 514
Views: 225,972
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