I have been working on RNA-Seq data from last 6 months, and i am able to crate accepted_hits.bam file for paired end data, but i am not able to create the accepted_hits.bam file for single end data using Tophat.
The commad line i used for single end data is:
Tophat -p 12 -G hg19.gtf -o C1_R1_thout genome SRR154213.fastq
Tophat -p 12 -G hg19.gtf -o C1_R2_thout genome SRR154214.fastq
after running this command i got the accepted_hits.bam which is of 600 byte size file which is not correct aligned file..
please let me know if i have to change the command line arguments ..