Hi,
I'm using TopHat v1.4.1 in order to analyze paired-end reads (75-35) in color space.
My tipical command line is:
tophat -G $annotation_file -C --no-coverage-search --library-type fr-secondstrand -g 10 -p 12 -r 90 -o $output_dir $reference_file $sample.F3.csfasta $sample.F5.csfasta
It works right but I have realized that Mapping QV of each read is either 80 or 0 (using QC tools after alignment). No other value.
In your opinion, what are the causes of that (How does Tophat algorithm work???)?
Do I have to modify Tophat command?
Thank a lot
Mattia
I'm using TopHat v1.4.1 in order to analyze paired-end reads (75-35) in color space.
My tipical command line is:
tophat -G $annotation_file -C --no-coverage-search --library-type fr-secondstrand -g 10 -p 12 -r 90 -o $output_dir $reference_file $sample.F3.csfasta $sample.F5.csfasta
It works right but I have realized that Mapping QV of each read is either 80 or 0 (using QC tools after alignment). No other value.
In your opinion, what are the causes of that (How does Tophat algorithm work???)?
Do I have to modify Tophat command?
Thank a lot
Mattia