![]() |
|
![]() |
||||
Thread | Thread Starter | Forum | Replies | Last Post |
Minimal FPKM values for analysis in Cufflinks | AdamB | Bioinformatics | 4 | 07-24-2013 12:48 AM |
Different FPKM values of cufflinks and cuffdiff | mrfox | Bioinformatics | 5 | 10-17-2012 02:10 PM |
Cufflinks and cuffdiff FPKM values | combiochem | Bioinformatics | 12 | 10-14-2012 12:37 AM |
cufflinks-1.0.3 produces very high FPKM values when compared to cufflinks-0.9.3. Why? | pinki999 | Bioinformatics | 5 | 06-09-2012 07:48 AM |
Different FPKM values of cufflinks and cuffdiff in latest version | mrfox | Bioinformatics | 1 | 11-23-2010 06:23 AM |
![]() |
|
Thread Tools |
![]() |
#1 |
Junior Member
Location: New Haven Join Date: Jun 2010
Posts: 6
|
![]()
Dear all,
I am using the latest versions of tophat (as of today) to map a non-model organism's transcriptome to a closely related model organism's genome. After trying almost all available parameters in Tophat, I was only able to get FPKM values for 170 genes (the model organism has ~17,000 genes) as cufflinks output. This led me to do separate alignments with Bowtie and once that was fed into cufflinks, I get FPKM values for ~5,000 genes. Now, my question is I would like to utilize the isoforms detected by Tophat, however I am not sure how to correctly calculate the FPKM values for the genes that I got reads mapped by both bowtie and tophat. Any help is greatly appreciated. Thanks. |
![]() |
![]() |
![]() |
Thread Tools | |
|
|