SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 8 of 8
Search took 0.00 seconds.
Search: Posts Made By: burt
Forum: Bioinformatics 08-23-2011, 11:59 PM
Replies: 0
Views: 2,814
Posted By burt
Cufflinks' computation of FPKM for --GTF and --GTF-guide estimation

Hi,

I was wondering if someone in the community would be able to shed some light on how Cufflinks compute the FPKM values when run under the --GTF and --GTF-guide modes.

From my understanding...
Forum: Bioinformatics 06-07-2011, 02:10 AM
Replies: 6
Views: 4,727
Posted By burt
[Cufflinks] Multi-Hit error

Hi, I'm running the latest build of Cufflinks (v1.0.3) on an Illumina paired-end RNA-seq library and its throwing me an error.

[chiakhb@pegasus biasCorrect_multiRead]$ cufflinks --output-dir...
Forum: Bioinformatics 04-12-2011, 07:22 PM
Replies: 16
Views: 4,799
Posted By burt
I'm having the same problem too.

I'm having the same problem too.
Forum: Bioinformatics 04-11-2011, 05:43 PM
Replies: 11
Views: 11,000
Posted By burt
Hi, thanks for the reply. My input data is a set...

Hi, thanks for the reply. My input data is a set of single-end reads. I'm pretty sure if a problem with the sam output in colorspace.

Just something to add on to the problem description. If I were...
Forum: RNA Sequencing 04-08-2011, 12:22 AM
Replies: 3
Views: 3,232
Posted By burt
Hey, I've been playing around with trans-abyss...

Hey, I've been playing around with trans-abyss for RNA-seq data. Erm, what mode/stage of trans-abyss did you ran? I don't seem to remember coming across those kind of output for trans-abyss.

In...
Forum: Bioinformatics 04-06-2011, 11:13 PM
Replies: 11
Views: 11,000
Posted By burt
Error in bowtie's sam output?

Hi,

I'm not sure if its a bug with the bowtie's sam output, but all my mapping quality would take the value of 255 while the bit flag would take on values of either 0,4,16. I had run bowtie in...
Forum: Bioinformatics 01-25-2011, 10:27 PM
Replies: 4
Views: 4,280
Posted By burt
I've got the same error.

I've got the same error.
Forum: Bioinformatics 01-16-2011, 06:06 PM
Replies: 0
Views: 2,577
Posted By burt
Understanding GSNAP output

Hi,

I'm trying out GSNAP as part of the analysis to look for fusion genes and novel transcripts.

I've ran GSNAP with and without the -N parameter. My question is surrounding the output of...
Showing results 1 to 8 of 8

 


All times are GMT -8. The time now is 11:09 PM.


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