tophat, --mate-inner-dist and variable length reads

[dawe]

Hi there, I have variable length RNA-seq reads ranging from 42 to 76 bp (I guess because of a trimming process). Since I have to specify --mate-inner-dist parameter, which would be the correct value?
Any hint is appreciated

d

[kmcarr]

Hi there, I have variable length RNA-seq reads ranging from 42 to 76 bp (I guess because of a trimming process). Since I have to specify --mate-inner-dist parameter, which would be the correct value?
Any hint is appreciated

d

I would suggest using some average value (mean, median, whatever) for --mate-inner-distance and accompanying that with an appropriate --mate-std-dev.

[dawe]

Good point, thanks!
Besides... I've realized I must know what trimming process has been applied. If 5' trimming, the inner size remains the same, if 3' trimming I will try to evaluate mean/stddev

d