Question: How To Set Tophat Insert Size Without A 'Test' Run?
gravatar for mengqingying
6.8 years ago by
United States
mengqingying30 wrote:

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 • 2.1k views
ADD COMMENTlink modified 6.8 years ago by Irsan7.2k • written 6.8 years ago by mengqingying30
gravatar for Irsan
6.8 years ago by
Irsan7.2k wrote:

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

ADD COMMENTlink written 6.8 years ago by Irsan7.2k

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.

ADD REPLYlink modified 6.8 years ago • written 6.8 years ago by Ashutosh Pandey12k
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