Cufflinks Returned 0 Value In All Rpkms

Question: Cufflinks Returned 0 Value In All Rpkms

5.0 years ago by

Canada

Ly, Dao • 20 wrote:

Hi I have been trying to analyze a rat Solid SRA but I encountered a problem: cufflinks gave me 0 RPKM in all genes. Here is my workflow 1. Get data with EBI SRA: sent the fastaq file directly to galaxy 2. Fastaq groomer 3. Mapped with bowtie for Solid (paire-ended) with the built- in index rat rn5 as reference genome 4. Sam to Bam the bowtie mapping result 5. Cufflinks the bam file All RPKMs of gene expression and transcript expression have a 0 value even thought the RPKM status is OK. I used default setting for all jobs. Am I missing something? Any help, suggestion will be greatly appreciated. Thank you very much Best regards Dao

rna-seq alignment bowtie cufflinks • 1.1k views

ADD COMMENT • link •

modified 5.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.0 years ago by Ly, Dao • 20

5.0 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello, If the data is RNA from rat, then you will want to be using Tophat instead of Bowtie. Otherwise the data will not be mapped as spliced the results will be off in many ways (the fragments counts are a small symptom of a larger problem). You can use 'Tophat for SOLiD' on a suitable local or cloud Galaxy instance. It is available on the Test server, but tools are not supported here (we test/break things!) and the quotas are just 10G with an account. But maybe is a place to do a small trial run before committing to a cloud server. http://getgalaxy.org http://usegalaxy.org/cloud http://usegalaxy.org/toolshed More about RNA-seq is in our wiki and public server, including link- outs and tutorials, you can get started here: Example ? RNA-seq analysis tools: http://wiki.galaxyproject.org/Support#Interpreting_scientific_results See RNA-seq examples: http://wiki.galaxyproject.org/Learn#Other_Tutorials Best, Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD COMMENT • link written 5.0 years ago by Jennifer Hillman Jackson ♦ 25k

5.0 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi Dao, To run the analysis correctly on SOLiD data, a local or cloud Galaxy would be needed. A cloud Galaxy is web based and if you follow the links below, you will find exact instructions for getting set up. There are Amazon fees, but they do have various grant programs that you can review at their site for help with that. Galaxy itself is always free!! About tools on the Test server .. these are constantly in flux in terms of dependencies and such, and we don't support them because this is truly a development environment for us. You may find that certain tools, including this one, work on smaller datasets at some point in the future, but for the public this shouldn't be used for serious work. One last option, and I don't know for certain if there is one in here that will accept your datatype and enough quota to do significant work (these also change over time), are other public Galaxy servers. Each is supported by the hosting group. A list is here and you can look through/review the sites to see what is available: http://wiki.galaxyproject.org/PublicGalaxyServers Take care, Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD COMMENT • link written 5.0 years ago by Jennifer Hillman Jackson ♦ 25k

Please log in to add an answer.

Similar posts • Search »