The order of part processions of RNA-Seq data

Question

[1106518271]

From the bam file file.bam (mapping by star) to htseq-count input data:

What's the order of the following steps in general？

a. sorted file.bam by name to get file.sorted.bam
b. index the file.bam or c. index the file.sorted.bam
d. get unique mapping reads from ?.bam

Thanks in advance!

Answer 1

[WouterDeCoster]

Please follow guidelines such as:

RNA-Seq workflow: gene-level exploratory analysis and differential expression