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
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