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Forum: Bioinformatics 04-21-2016, 08:30 AM
Replies: 2
Views: 1,097
Posted By kajot
As always very helpful, Devon, I owe you few...

As always very helpful, Devon, I owe you few beers already;)

Thanks for the tip!
Forum: Bioinformatics 04-20-2016, 06:48 AM
Replies: 2
Views: 1,097
Posted By kajot
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...
Forum: Bioinformatics 03-07-2016, 06:40 AM
Replies: 2
Views: 1,903
Posted By kajot
I found the problem, I was using wrong GTF...

I found the problem, I was using wrong GTF annotation, should've used GENCODE mouse M1 since vM3 is built on mm10...
Forum: Bioinformatics 03-06-2016, 04:42 AM
Replies: 2
Views: 1,903
Posted By kajot
Subread low percentage of assigned fragments in ENCODE data

Hi there guys!


I am using Subread v1.5.0-p1 to get tables of counts for RNAseq data I got from ENCODE (https://www.encodeproject.org/experiments/ENCSR000BYX/).
What I am trying to get are...
Forum: Bioinformatics 11-21-2014, 08:48 AM
Replies: 12
Views: 9,176
Posted By kajot
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...
Forum: Bioinformatics 11-20-2014, 09:45 AM
Replies: 12
Views: 9,176
Posted By kajot
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...
Forum: Bioinformatics 11-20-2014, 08:45 AM
Replies: 12
Views: 9,176
Posted By kajot
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...
Forum: Bioinformatics 10-13-2014, 06:28 AM
Replies: 1
Views: 1,743
Posted By kajot
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...
Forum: RNA Sequencing 05-07-2014, 07:49 AM
Replies: 0
Views: 1,274
Posted By kajot
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...
Forum: RNA Sequencing 04-07-2014, 05:45 AM
Replies: 6
Views: 3,031
Posted By kajot
Ok, all is clear, I am deeply grateful for your...

Ok, all is clear, I am deeply grateful for your help :)
Forum: RNA Sequencing 04-07-2014, 05:41 AM
Replies: 6
Views: 3,031
Posted By kajot
I understand, I wasn't sure since in my .gtf file...

I understand, I wasn't sure since in my .gtf file there are entries like this:

1 protein_coding exon 4830268 4830315 . + . exon_id "ENSMUSE00001118471"; exon_number...
Forum: RNA Sequencing 04-07-2014, 12:56 AM
Replies: 6
Views: 3,031
Posted By kajot
That's very concise and informative. Thank you...

That's very concise and informative. Thank you for the answer !


However, one more thing troubles me, I have an Ensembl GRCm38 .gtf file that contains in 3rd column values such as exon, CDS,...
Forum: RNA Sequencing 04-04-2014, 08:51 AM
Replies: 6
Views: 3,031
Posted By kajot
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...
Forum: RNA Sequencing 04-02-2014, 09:21 AM
Replies: 6
Views: 4,975
Posted By kajot
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...
Forum: RNA Sequencing 04-01-2014, 08:05 AM
Replies: 6
Views: 4,975
Posted By kajot
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,...
Forum: Introductions 04-01-2014, 06:43 AM
Replies: 0
Views: 986
Posted By kajot
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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