Forum: Bioinformatics
04-21-2016, 07:30 AM
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Replies: 2
Views: 1,194
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Forum: Bioinformatics
04-20-2016, 05:48 AM
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Replies: 2
Views: 1,194
Quantifying ChIPseq signal for one sample
Hey Everybody,
I am trying to rank genes according to their phosphorylated CTD Pol II occupancy as a rough estimate of ongoing transcription.
I am using ENCODE Pol2 ChIPseq data, which means I...
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Forum: Bioinformatics
03-07-2016, 05:40 AM
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Replies: 2
Views: 2,085
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Forum: Bioinformatics
03-06-2016, 03:42 AM
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Replies: 2
Views: 2,085
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Forum: Bioinformatics
11-21-2014, 07:48 AM
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Replies: 12
Views: 9,557
So the more "flat" coverage I get towards the...
So the more "flat" coverage I get towards the center of the intron, the more reliable indication this is that I am dealing with a legitimate intron retention ? Is my understanding right ?
And...
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Forum: Bioinformatics
11-20-2014, 08:45 AM
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Replies: 12
Views: 9,557
I am not sure if my quick coverage look-up for...
I am not sure if my quick coverage look-up for those introns makes sense, maybe this would be important - I took an average of counts from all conditions for any given intron and divided this value...
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Forum: Bioinformatics
11-20-2014, 07:45 AM
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Replies: 12
Views: 9,557
Hi
I tried the script from Devon, thanks...
Hi
I tried the script from Devon, thanks AGAIN for help ;) It works nicely and I managed to run DEXSeq with the new intronic annotation. I decided to delete exons and rename introns to...
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Forum: Bioinformatics
10-13-2014, 05:28 AM
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Replies: 1
Views: 1,881
Calculating PSI values for rat RNA-seq
Hi,
could someone recommend me something to calculate Percent Spliced-In (PSI) values for all the exons of rat in a paired-end RNA-seq experiment ?
I tried out MISO, but it seems to me that...
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Forum: RNA Sequencing
05-07-2014, 06:49 AM
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Replies: 0
Views: 1,328
DEXSeq - glm fit failed for gene (...)
Welcome!
I am struggling with an error I get while trying to call function plotDEXSeq for a giant gene (titin). My data are very rich (high sequencing depth, multiple biological replicates) and I...
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Forum: RNA Sequencing
04-07-2014, 04:45 AM
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Replies: 6
Views: 3,131
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Forum: RNA Sequencing
04-07-2014, 04:41 AM
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Replies: 6
Views: 3,131
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Forum: RNA Sequencing
04-06-2014, 11:56 PM
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Replies: 6
Views: 3,131
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Forum: RNA Sequencing
04-04-2014, 07:51 AM
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Replies: 6
Views: 3,131
DESeq2 - understanding multi-factor DE analysis
Hello again dear SeqAnswers,
I have another question regarding RNA-seq data processing, this time with DESeq. I had count tables from my experiment generated successfully by DEXSeq counting...
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Forum: RNA Sequencing
04-02-2014, 08:21 AM
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Replies: 6
Views: 5,207
Thank you for all your rapid replies! I was...
Thank you for all your rapid replies! I was swamped today with regular wet-lab work so I had little time to check all your suggestions, I will try to re-run counting script with -p reverse tomorrow...
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Forum: RNA Sequencing
04-01-2014, 07:05 AM
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Replies: 6
Views: 5,207
DEXseq - very low numbers of counts
Hello,
I wanted to ask the community for help with my problem related to using DEXseq, particularily generating count tables with the Python script. My problem is as follows:
I have paired-end,...
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Forum: Introductions
04-01-2014, 05:43 AM
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Replies: 0
Views: 1,047
Hello! No life story, just saying "hi"
Dear SEQanswers forum,
I am reading numerous topics on this portal since few months now, but never started any topic myself (or contributed to already existing ones). Since I ran into some...
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