I am new tophat user, I run my first RNA-seq, by using an already published data to test. However I have got 0.0% mapping rate. Obviously I am making a mistake.
The data that I am using is strand specific RNA-seq. I used the GEOdatabase to access the data. I run my tophat based on options they provide in the paper with following command:
tophat2 -r 25 --coverage-search -G UCSC/refGene_mm9.gtf --library-type fr-firststrand /bowtie2/mm9 subset697.fastq &> tophat.log
I was looking at the Nature Protocols paper for tophat and I realize that in the paper, for strand specific data, they provide 2 different fastq file.I think that is the problem in my case. I only have left_reads in my tmp folder. Does anybody have experience on strand-specific RNA-seq? And if I need two fastq file, any ideas what can I do about it since the data on GEOdatabase contains 1 big fastq file?
Thank you!! -A