Alignment prior to passing SAM/BAM to DEXSeq

Question

[wiscoyogi]

For passing BAM/SAM files to DEXSeq. I understand that this program will take input bam/sam files that were generated using a genome aligner (eg STAR, etc).

Question: are there specific recommendations/guidance for the associated run mode on a given aligner, especially for STAR with one pass or two pass (eg --twopassMode Basic)?

Thank you

[GenoMax]

If you are not interested in identifying novel junctions you could do a normal one pass mapping.

Answer 1

[james.hawley]

There are some specific recommendations about different parameters in the STAR manual. Check out Chapter 8 for counting reads per gene, and Chapter 17 for more detailed descriptions of the CLI parameters.