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Old 08-16-2015, 11:07 PM   #1
frymor
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Location: Germany

Join Date: May 2010
Posts: 150
Default different read lengths in rna-star

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
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