How To Set Tophat Insert Size Without A 'Test' Run?

Question

[mengqingying]

correctly setting 2 parameters in Tophat: --mate-inner-dist --mate-std-dev should be very important, but i have no idea how to set them without firstly running bowtie (or bowtie2) -> samtools -> picard tools, which seems a little bit redundant for Tophat.

Does any one have suggestions? Thanks in advance!!

Answer 1

[Irsan]

During sample preparation you/your lab has probably used bioanalyzer to quality control the sample. In those results you can estimate the fragment size and its standard deviation from the histogram

[Ashutosh Pandey]

Yes the best way would be to ask the person who handled the sequencing part. Otherwise, the only way would be to map a few reads. Take the first 10,000-20,000 reads and then map then and estimate the mean insert size. Your insert size need not to be accurate and a rough estimation should be enough for the aligner.