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Search: Posts Made By: am@i
Forum: Bioinformatics 03-03-2015, 08:36 PM
Replies: 24
Views: 9,848
Posted By am@i
Thank you @devon

Thank you @devon
Forum: Bioinformatics 02-11-2015, 06:19 AM
Replies: 24
Views: 9,848
Posted By am@i
Hello, I find the XS tag filtering the aligned...

Hello,
I find the XS tag filtering the aligned discordantly 1 time reads.

Thanks
Amrita
Forum: Bioinformatics 05-15-2014, 12:05 AM
Replies: 3
Views: 2,215
Posted By am@i
Hello everyone, I want to compare snpeff result...

Hello everyone,
I want to compare snpeff result between two samples. ANy recommendations for softwares for this? I obviously will compare SNP and INDELS etc?

Thank You in advance :)
Forum: Bioinformatics 04-17-2014, 11:07 PM
Replies: 10
Views: 3,532
Posted By am@i
Thanks for d reply!! :) I have another...

Thanks for d reply!! :)
I have another questions ...

When I compare the assembled transcripts with a reference annotation with cuffcompare, one of the output files is cuff_in.tmap. According to...
Forum: Bioinformatics 04-16-2014, 12:35 AM
Replies: 10
Views: 3,532
Posted By am@i
Hello Everyone, I have been running the...

Hello Everyone,
I have been running the tophat->cufflinks->cuffcompare software in order to find novel transcripts!! This is a some part of my cuffcompare results:

...
Forum: Bioinformatics 04-15-2014, 05:47 AM
Replies: 10
Views: 3,532
Posted By am@i
novel transcript in cuffcompare data

hello, all

how i can identify novel transcript when i run cuffcompare ???
tophat -o output arabidopsis.fa file1_R1.fq file1_R2.fq
cufflinks -o output accepted_hits.bam
cuffmerge -s...
Forum: Bioinformatics 04-15-2014, 04:36 AM
Replies: 2
Views: 2,402
Posted By am@i
hello Devon, how i can identify novel...

hello Devon,

how i can identify novel transcript when i run cuffcompare ???
tophat -o output arabidopsis.fa file1_R1.fq file1_R2.fq
cufflinks -o output accepted_hits.bam
cuffmerge -s...
Forum: Bioinformatics 03-27-2014, 05:59 AM
Replies: 22
Views: 4,404
Posted By am@i
I used this command :- cds2 <-...

I used this command :-
cds2 <- estimateDispersions( cds2, method="blind", fitType="local", sharingMode="fit-only" )
res2 = nbinomTest( cds2, "control", "treatment" )
Forum: Bioinformatics 03-27-2014, 04:27 AM
Replies: 22
Views: 4,404
Posted By am@i
please find the attached count file of miRNA....

please find the attached count file of miRNA. many counts seem to be vastly different but still i am getting non-significant DE.
kindly suggest!
Forum: Bioinformatics 03-27-2014, 04:02 AM
Replies: 22
Views: 4,404
Posted By am@i
Ok forget about other tests, my problem is DEseq...

Ok forget about other tests, my problem is DEseq gives all the p- values and FDR values as non-significant while performing DE analysis of miRNA seq from illumina (which should not be the case...
Forum: Bioinformatics 03-26-2014, 09:30 PM
Replies: 22
Views: 4,404
Posted By am@i
hi Simon Thanks for the last reply !!! I have...

hi Simon
Thanks for the last reply !!!
I have another query?
I am getting all the p- values and FDR values as non-significant while performing DE analysis of miRNA's in DEseq. Whereas almost all...
Forum: Bioinformatics 03-26-2014, 04:32 AM
Replies: 4
Views: 5,951
Posted By am@i
Hi I am getting all the p- values and FDR...

Hi
I am getting all the p- values and FDR values as non-significant while performing DE analysis of miRNA's in DEseq. Whereas almost all are significant with chi-square test.What is the reason for...
Forum: Bioinformatics 03-26-2014, 03:31 AM
Replies: 22
Views: 4,404
Posted By am@i
hi I am performing DE analysis using DEseq. In...

hi
I am performing DE analysis using DEseq. In a DE analysis suppose the control has a read count value zero (0) and treatment has some number (=>1) then the DE will always be infinity. In such a...
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