What is the significance of sjdbOverhang when generating a genome?

[Alexandria Pinto]

Hi Alex,

I was wondering what would happen if we align a 2x150b paired end read on a genome generated with --sjdbOverhang=100? What would happen if we align a 2x75b paired end read on the same genome? 

How does this effect alignment overall? 

In my analysis, I am seeing that the 2x150b reads seem to spill over the exon into intronic regions, while the 2x75b seem to stay tightly in the exon boundaries. 

Thanks for the help (again)!

Alex

[Alexander Dobin]

Hi Alexandria,

the --sjdbOverhang value should have marginal effect on the alignments.

You can check that by generating the genome with "ideal" values --sjdbOverhang 74 for the 75b reads and 149 for 150b reads.

I do not think the effect you are seeing will change substantially, but it's always better to check. :)

Cheers

Alex