SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 7 of 7
Search took 0.00 seconds.
Search: Posts Made By: avi
Forum: Bioinformatics 04-03-2013, 02:09 PM
Replies: 0
Views: 969
Posted By avi
Question Transcripts missing from Cufflinks FPKMtracking file. Run with -G option

Hi,

I am using Cufflinks with the -G option to get the FPKM values of all transcripts specified in the Ensembl annotation file. But when I look at the isoforms.FPKM_tracking file, I see that some...
Forum: Bioinformatics 10-03-2011, 01:39 PM
Replies: 20
Views: 5,265
Posted By avi
Hi Hunny, Thats what I originally thought...

Hi Hunny,

Thats what I originally thought too. But apparently it doesn't work that way. From what I understand, during the processing for RNAseq, the RNA is converted into double stranded cDNA and...
Forum: Bioinformatics 09-29-2011, 08:43 AM
Replies: 20
Views: 5,265
Posted By avi
Hi joro, No, i still didn't get any answers...

Hi joro,

No, i still didn't get any answers to how Cufflinks does its strand calling for single exon transcripts.

But when I looked at the "wrong" strand assigned transcripts, I found that a...
Forum: RNA Sequencing 09-28-2011, 03:18 PM
Replies: 0
Views: 1,327
Posted By avi
Transcript mapping stats from Cuffcompare - Does this look right to you?

Hi all,

I am working on some RNAseq data (Single end reads,36 bp from an Illumina instrument) from a prostrate cancer cell line. All I have for this is a Fasta file of all the reads.

I have...
Forum: Bioinformatics 06-20-2011, 07:21 PM
Replies: 20
Views: 5,265
Posted By avi
Question Question about Cufflink strand calling

Hi all,

I have 2 questions about strand calling..

1) From what I understand, if using an unstranded library protocol, there is no way to directly tell which strand a transcript is from just...
Forum: Bioinformatics 06-01-2011, 06:37 PM
Replies: 2
Views: 2,347
Posted By avi
Question Missing Junctions in Tophat! ( after providing a known junctions & gene models files)

I am using Tophat for aligning unpaired RNAseq reads (36 bases each) and I had a question about junction calling in Tophat. I tried running Tophat with both -j (a known junctions file from Ensembl)...
Forum: Bioinformatics 04-04-2011, 11:55 AM
Replies: 2
Views: 2,164
Posted By avi
Question Scripture -windows argument

Hi,

I am new to next-gen sequencing, so this might be a very obvious question. But still..

I am trying to use Scripture for my work. But I am not able to figure out how the -windows argument...
Showing results 1 to 7 of 7

 


All times are GMT -8. The time now is 07:40 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO