different read lengths in rna-star

[frymor]

Hi,

I have a data set with several samples of length 76 and others of read length of 100 bases.

I would like to analyse them using the star aligner, But I am not sure how to create the indexed genome.

While creating the index one should use the parameter sjdbOverhang with the value of ReadLength-1.

I know I can use max(ReadLength)-1, but as in the newer versions of RNA Star there is the possibility to use these parameters also on the fly while mapping, I would like to know if it is necessary at all to use them while indexing.

Is it a good idea to run the indexing with them and than again use them while mapping, or can it even cause problems?

thanks
Assa