On 7/1/12 8:30 PM, Paul
Hello Jennifer, I was hoping you could enlighten me about a problem I am currently having. I have two rna-seq datasets that I am trying to evaluate using cufflinks - I keep getting null sets back with the second set, no matter what I do. I am pretty sure that the data are identical in nature, just from different conditions. Is there an issue with the current cufflinks instance? Or am I screwing up somehow. I am trying to evaluate item 149 from my history (which is the filtered and sorted set from Bowtie analysis). This should be identical in nature to item 113, with the only difference being the read source (same bug, different conditions). Both were mapped to the same ref genome (from the history) and the same annotation file (again, from the history). Any help is much appreciated!
-- Paul
-- Jennifer Jackson http://galaxyproject.org
Hello Paul, By "null values" I am guessing that you mean that the FPKM values are "0". http://cufflinks.cbcb.umd.edu/manual.html#transexpr This is an indication of a possible mismatch between the input BAM/SAM data and the reference annotation GTF file. You will need to double check that both of these are true between all inputs: 1 - the chromosome naming is identical 2 - the sort ordering is identical Our RNA-seq FAQ has items that cover both: https://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq If that does not resolve the issue, and there is no error dataset from Galaxy, you might consider the Cufflinks help email address next: tophat.cufflinks@gmail.com http://wiki.g2.bx.psu.edu/Support#Interpreting_scientific_results (see Example: unexpected results with RNA-seq analysis tools.) Best, Jen Galaxy team
I was hoping you could enlighten me about a problem I am currently having. I have two rna-seq datasets that I am trying to evaluate using cufflinks - I keep getting null sets back with the second set, no matter what I do. I am pretty sure that the data are identical in nature, just from different conditions. Is there an issue with the current cufflinks instance? Or am I screwing up somehow. I am trying to evaluate item 149 from my history (which is the filtered and sorted set from Bowtie analysis). This should be identical in nature to item 113, with the only difference being the read source (same bug, different conditions). Both were mapped to the same ref genome (from the history) and the same annotation file (again, from the history). Any help is much appreciated!
-- Paul
-- Jennifer Jackson http://galaxyproject.org
Hi Jennifer, thanks for the advice. you are right, I meant that the fpkm values are 0. I have checked the things you suggested, and everything matches up as far as I can tell. I will start over from the mapping and see if that helps. Thanks! Paul On Mon, Jul 2, 2012 at 10:57 AM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hello Paul,
By "null values" I am guessing that you mean that the FPKM values are "0". http://cufflinks.cbcb.umd.edu/**manual.html#transexpr<http://cufflinks.cbcb.umd.edu/manual.html#transexpr>
This is an indication of a possible mismatch between the input BAM/SAM data and the reference annotation GTF file. You will need to double check that both of these are true between all inputs: 1 - the chromosome naming is identical 2 - the sort ordering is identical
Our RNA-seq FAQ has items that cover both: https://main.g2.bx.psu.edu/u/**jeremy/p/transcriptome-**analysis-faq<https://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq>
If that does not resolve the issue, and there is no error dataset from Galaxy, you might consider the Cufflinks help email address next: tophat.cufflinks@gmail.com http://wiki.g2.bx.psu.edu/**Support#Interpreting_**scientific_results<http://wiki.g2.bx.psu.edu/Support#Interpreting_scientific_results> (see Example: unexpected results with RNA-seq analysis tools.)
Best,
Jen Galaxy team
I was hoping you could enlighten me about a problem I am currently
having. I have two rna-seq datasets that I am trying to evaluate using cufflinks - I keep getting null sets back with the second set, no matter what I do. I am pretty sure that the data are identical in nature, just from different conditions. Is there an issue with the current cufflinks instance? Or am I screwing up somehow. I am trying to evaluate item 149 from my history (which is the filtered and sorted set from Bowtie analysis). This should be identical in nature to item 113, with the only difference being the read source (same bug, different conditions). Both were mapped to the same ref genome (from the history) and the same annotation file (again, from the history). Any help is much appreciated!
-- Paul
-- Jennifer Jackson http://galaxyproject.org
-- Paul Orwin, Ph.D. Associate Professor, Biology Department California State University, San Bernardino 5500 University Pkwy San Bernardino, CA, 92407 (909) 537-5405 porwin@csusb.edu
I tried it again, and everything seems to have worked. I suspect that I had the paired ends in the wrong order, which screwed up the alignment with the annotated genome. Thanks for helping! On Mon, Jul 2, 2012 at 11:31 AM, Paul Orwin <porwin@csusb.edu> wrote:
Hi Jennifer, thanks for the advice. you are right, I meant that the fpkm values are 0. I have checked the things you suggested, and everything matches up as far as I can tell. I will start over from the mapping and see if that helps. Thanks! Paul
On Mon, Jul 2, 2012 at 10:57 AM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hello Paul,
By "null values" I am guessing that you mean that the FPKM values are "0". http://cufflinks.cbcb.umd.edu/**manual.html#transexpr<http://cufflinks.cbcb.umd.edu/manual.html#transexpr>
This is an indication of a possible mismatch between the input BAM/SAM data and the reference annotation GTF file. You will need to double check that both of these are true between all inputs: 1 - the chromosome naming is identical 2 - the sort ordering is identical
Our RNA-seq FAQ has items that cover both: https://main.g2.bx.psu.edu/u/**jeremy/p/transcriptome-**analysis-faq<https://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq>
If that does not resolve the issue, and there is no error dataset from Galaxy, you might consider the Cufflinks help email address next: tophat.cufflinks@gmail.com http://wiki.g2.bx.psu.edu/**Support#Interpreting_**scientific_results<http://wiki.g2.bx.psu.edu/Support#Interpreting_scientific_results> (see Example: unexpected results with RNA-seq analysis tools.)
Best,
Jen Galaxy team
I was hoping you could enlighten me about a problem I am currently
having. I have two rna-seq datasets that I am trying to evaluate using cufflinks - I keep getting null sets back with the second set, no matter what I do. I am pretty sure that the data are identical in nature, just from different conditions. Is there an issue with the current cufflinks instance? Or am I screwing up somehow. I am trying to evaluate item 149 from my history (which is the filtered and sorted set from Bowtie analysis). This should be identical in nature to item 113, with the only difference being the read source (same bug, different conditions). Both were mapped to the same ref genome (from the history) and the same annotation file (again, from the history). Any help is much appreciated!
-- Paul
-- Jennifer Jackson http://galaxyproject.org
-- Paul Orwin, Ph.D. Associate Professor, Biology Department California State University, San Bernardino 5500 University Pkwy San Bernardino, CA, 92407 (909) 537-5405 porwin@csusb.edu
-- Paul Orwin, Ph.D. Associate Professor, Biology Department California State University, San Bernardino 5500 University Pkwy San Bernardino, CA, 92407 (909) 537-5405 porwin@csusb.edu
participants (2)
-
Jennifer Jackson -
Paul Orwin