From: Noa Sher <noa.sher@gmail.com>
To: Bomba Dam <bomba.dam@visva-bharati.ac.in>
Cc: galaxy-user@lists.bx.psu.edu
Sent: Wednesday, February 22, 2012 7:28 AM
Subject: Re: [galaxy-user] Cufflinks related
problem
Hi Bomba
I cant know for sure without seeing your files but I originally
had the same problem and it ended up being because the way the
genome was named in the fasta genome file was not the same as the
way it was named in column 1 of my gtf file. I would check that
first. Also- with bacteria you dont want to run cufflinks with
default parameters- use the galaxy browser to check how your data
looks after tophat and you will most likely see very strange
gene-spanning introns. Change the max intron size to 1000-1500 and
the min distnace to 101-5nt and you should get results that make
much more sense.
Good luck
Noa
On 22/02/2012 00:12, Bomba Dam wrote:
Dear Noa,
Can you please tell me the parameters that I should keep while
mapping bacterial transcripts using cuffkins. I have kept the
default parameters as in Cufflinks and used my custom genome
annotation in gff3 format. The cufflinks seems to work Ok but all
the FPKM values in these files are zero. As suggested by other
users I have checked the correctness of my GFF3 files. The
corresponding fasta file was used for mapping the transcripts
using Bowtie. Are there any special trick for mapping bacterial
transcriptome.
regards,
Bomba
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