isaacvock
commented
2 days ago The developers will probably have more to say, but I will quickly point out that GRAND-SLAM has a boolean parameter named "introns", that if activated will "Compute introns", which I assume means not throwing out intronic reads when estimating NTRs.
With respect to "what you are looking at" with your current analysis output, without --introns in your call to GRAND-SLAM, I am guessing that differences in yours and GRAND-SLAM's strategies for identifying intronic reads may be leading to some of the reads in your bam file of intron mapping reads getting flagged as exonic and thus used to estimate NTRs.
Best, Isaac
Hello Florian,
in the description of the output table you say "intronic reads are not considered (as they would bias the NTR)". However, I split my bams in reads mapping on exons and reads mapping on introns and then I ran GRAND-SLAM and obtained the results. So, if intronic reads are discarded in the count of NTR, what am I looking at? I'd need the NTR both from exonic and intronic reads. Thanks in advance,
Valeria