Getting libType without running quantification with Salmon

Question

[compuTE]

I want to use Salmon just to check the strandness of my samples. Is there a way to get the guess of libtype (--libType A) without getting all the output from the quantification? Or skipping running the quantification all-together?

Answer 1

[ATpoint]

https://salmon.readthedocs.io/en/latest/salmon.html#skipquant

[compuTE]

Whoops, I guess I missed reading this. Thanks.

[Rob]

Also, it's worth noting that to estimate the strandedness of the library, it's not necessary for salmon to look at all of the reads if you're not attempting to perform quantification. So, you could do something like passing only the first million reads to salmon along with the --skipQuant option, and then you can see what library type it guessed. Since salmon can read from named pipes, you can accomplish this with something like -1 <(gunzip -c fastq_1.fq.gz | head -n 4000000) -2 <(gunzip -c fastq_2.fq.gz | head -n 4000000) to only pass the first million records of the fastq files to salmon.