Now I am using tophat version 1.3.2 and my data is paired-end 100bp reads.
My question is : why --mate-inner-dist and --mate-std-dev can affect the tophat hit number? According to my knowledge about tophat, these two parameter should only affect the second column of sam/bam output.
Look forward to your response and thanks in advance
My question is : why --mate-inner-dist and --mate-std-dev can affect the tophat hit number? According to my knowledge about tophat, these two parameter should only affect the second column of sam/bam output.
Look forward to your response and thanks in advance