Cufflinks

6.4 years ago by

United States

Jennifer Hillman Jackson ♦ 25k 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 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 -- Jennifer Jackson http://galaxyproject.org

ADD COMMENT • link written 6.4 years ago by Jennifer Hillman Jackson ♦ 25k

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 -- 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

ADD REPLY • link written 6.4 years ago by Paul Orwin • 20

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! -- 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

ADD REPLY • link written 6.4 years ago by Paul Orwin • 20

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