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

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


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?

frymor is offline   Reply With Quote

mapping, read length, star aligner

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