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
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
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