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Forum: RNA Sequencing 07-14-2015, 07:19 PM
Replies: 89
Views: 33,120
Posted By mfahim
After applying most of the solutions mentioned...

After applying most of the solutions mentioned above.. I am still getting this message..

Error : objects ‘metadata’, ‘isTRUEorFALSE’, ‘isSingleString’ are not exported by 'namespace:IRanges'...
Forum: RNA Sequencing 06-28-2015, 05:13 PM
Replies: 0
Views: 657
Posted By mfahim
SpliceR- Splice Graphs and Alternative Splicing

Hi everyone,

Has anyone used spliceR for RNA-seq in Arabidopsis?.
If yes, then kindly tell me how to assign a browser other than UCSC as they dont have Arabidopsis in their stash.

Cheers
Forum: RNA Sequencing 06-12-2015, 12:40 AM
Replies: 2
Views: 968
Posted By mfahim
I got an excellent explanation to my querry..

https://www.biostars.org/p/146223/#146242
Forum: RNA Sequencing 06-11-2015, 10:04 PM
Replies: 2
Views: 968
Posted By mfahim
Problems with q-value in RNAseq

I have four subjects (one wildtype and three mutants, no replications) at two different conditions (a total of 8 samples).. cuffdiff tells me there is no significant difference based on adjusted...
Forum: RNA Sequencing 06-07-2015, 06:17 AM
Replies: 1
Views: 1,813
Posted By mfahim
updates

Hi there, I hope you have resolved your issue.

I am using pair-end reads from four samples (one control, three treatments). I aligned both right and left files together. I managed through tophat2....
Forum: Bioinformatics 04-29-2015, 11:33 PM
Replies: 313
Views: 90,532
Posted By mfahim
Smile Bingo!! Thank you Simon

for the Genelist..
That is exactly what I was looking for. Perfect.

More questions next week... :)

Cheers
Fahim
Forum: Bioinformatics 04-29-2015, 09:19 PM
Replies: 313
Views: 90,532
Posted By mfahim
Suggestion for next version of SeqMonk

Hi Simon,
Like many others on this forum, I am a big fan of SeqMonk.
Here is a suggestion for next version (or may be I dont understand SeqMonk).
Yes, we can make customized Annotation Tracks BUT...
Forum: Bioinformatics 04-27-2015, 02:19 AM
Replies: 313
Views: 90,532
Posted By mfahim
1. is this RNA-Seq or small RNA? Ans.Yes, this...

1. is this RNA-Seq or small RNA?
Ans.Yes, this is smallRNA seq.

2. What is the quantitation?
Ans. As you mentioned previously, I applied the normal RNAseq Quantitation pipeline.

3. Did you...
Forum: Bioinformatics 04-27-2015, 01:31 AM
Replies: 313
Views: 90,532
Posted By mfahim
Oh. previous snapshot was too big perhaps..here...

Oh. previous snapshot was too big perhaps..here is another one. Cheers
Forum: Bioinformatics 04-26-2015, 06:34 PM
Replies: 313
Views: 90,532
Posted By mfahim
Thanks Simon---However

Thanks for the tip off.. Howerver, I am a bit worried about the cummulative distribution graph after percentile re-quantitation and match distribution quantitation. here is the snapshot.
Forum: Bioinformatics 04-24-2015, 06:35 PM
Replies: 313
Views: 90,532
Posted By mfahim
smallRNA Analysis Pipeline

Hi Simon.
introducing RNAseq quantitation pipeline to seqmonk is great. Are you planning to add a pipeline for smallRNA soon?. If not how do I define probe for small RNAs.

Thanks
Fahim
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