Please help me to sort out this problem.
Why showing 0.0% overall read mapping rate????
My result given below:
Input : 238477
Mapped : 2 ( 0.0% of input)
0.0% overall read mapping rate.
Well, your first 2 problems are: 1) this is not a “tool” post, and 2) don’t use tophat
use STAR or HISAT2. Tophat is out of date.
I have changed this thread from a "Tool" to a "Question".
Post your code to understand what is going on.
$ tophat -G '/home/amit/Desktop/ngs new/archive-2010-09-27-22-25-17/genes.gtf' -o tophat16_2 bowtie2index SRR01545.fastq
Try to use tophat2 instead of tophat if tophat usage is
$ tophat2 -o tophat16_2 -G /home/amit/Desktop/ngs new/archive-2010-09-27-22-25-17/genes.gtf bowtie2index .SRR01545.fastq
Thank you for giving valuable time.
To my understanding, code seems to be fine considering above. I guess you have correct files in place and your GTF file annotations from hg19. GTF need not be in quotes.
Independently, take 5 or more reads (sequences) and blast against human genome. Check where they align. Sample your fastq ( some thing like 10%) and try to align instead of entire fastq. See if that works with tophat2.