I need some help trying to know how to analyze RNA-Seq data from ABI 5500 solid sequencing data.
I need to develop the following pipeline:
- Download data from GEO GSE39860 - done using ascp - no need for help here. The data was downloaded from here.
- Use SRA toolkit to transform the data into color fasta, qualities or some file format that tophat can run - here I have spent most of the time without luck! Any ideas on which command to use from the SRA toolkit to get the data in a good format for TopHat?
- How to properly run Tophat with the previous data?
for 3, once I have a good command for the SRA part 2 I plan to run the following command for tophat, does it look good?
module load bio/bowtie-0.12.7
module load bio/tophat-2.0.4.Linux_x86_64
tophat2 --color --quals --library-type fr-secondstrand -G ucsc_mm9.gtf -o <pathtohere>/bowtie-indexes/mm9/mm9c <pathtohere>/fq/SRR534610.csfasta <pathtohere>/rnaseq/fq/SRR534610.qual
Please if anyone have some advice let me know, I'd be very glad to hear suggestions!