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After reading the manual, I still have some questions about running tophat & cufflinks, as following:
I am a bit confused with the options "anchor-length " and "segmet-length" when running tophat..
In my opinion, the default setting "--segment-length" 25 means a segment read no less than 25, and "--min-anchor-length " 8 means a cut of 8, which is smaller than 25, so what is the exact length of the final read? Is it 25 or 8? What is the specificity of using "--min-anchor-length "?
To address this question, I propose the following process to test a read length of 75, using the tophat mapped genome,
First, tophat will map initial reads to genome, the initial reads length is 75
Second, tophat will split all IUM reads into smaller segments to map again, now the length is at least 25
Final, still unmapped reads will map junctions in the tophat database of possible splice junctions, a mapped read longer than the "anchor length" will confirm a junction, am I right?
Thank you very much.
Best regards,
song
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