using sam files for feature counts, and confusion about strandedness

Question

[smithkthedale]

Can you use sam files for featureCounts or must you sort them to bam and then sorted bam? I see lots of different answers.

Also, I am using RF paired end files. Would my strandedness (-s) be 0, -1, -2? I have done a lot of reading and I think 0 is the correct answer, but am very confused what each means and need some help.

This is my script:

featureCounts -p -s 0 -T 10 -a Arabidopsis_300_v3.1.gene_exons.gff3.gtf -o featurecounts.txt hisatsamfiles/*.sam

I appreciate any help provided. I have tried to read the manual and look at other responses, but everything says something a little different.

Will like any answers!

Thanks!

Answer 1

[iraun]

Here you can find the manual of featureCounts.., where it says:

Input_files: Give the names of input read files that include the read mapping results. 
The program automatically detects the file format (SAM or BAM).

Regarding the strandness, as well, from the manual you can read:

Indicate if strand-specific read counting should be performed.
A single integer value (applied to all input files) or a string
of comma-separated values (applied to each corresponding input file) should be provided. 
Possible values include: 0 (unstranded), 1 (stranded) and 2 (reversely stranded).

0 means unstranded data.. and RF is definitely stranded.