Alignment prior to passing SAM/BAM to DEXSeq
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
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james.hawley •
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wiscoyogi •
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wiscoyogi •
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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.
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If you are not interested in identifying novel junctions you could do a normal one pass mapping.