Test-drive the GATK tools and Best Practices pipelines on Terra
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RNA Seq variant calling: correct values for second pass index generation
I have a question about https://www.broadinstitute.org/gatk/guide/article?id=3891 step 3: For the 2-pass STAR, a new index is then created using splice junction information contained in the file SJ.out.tab from the first pass:
the parameter --sjbdOverhang: I have paired-end 40M reads with 51bp insert size. What is the correct value for this parameter in this case? Is it 51 or 50? According to the manual of STAR, ideally the value for sjdbOverhang is mate_length-1. You guys recommend 75 for 75bp paired-end reads. Is this correct? First of all, is mate_length the same as insert size?
Thank you for your help in advance!