This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How To Set Tophat Insert Size Without A 'Test' Run?

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!!

rnaseq
• 2,924 views • link
updated by Irsan Irsan • written by mengqingying • mengqingying

1 answer

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

• 165 views • link
written by Irsan Irsan

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.

• 0 views • link
written by Ashutosh Pandey Ashutosh Pandey

Log in to answer this question.

More posts like this