mapping rate calculations warning about salmon HOT 2 CLOSED

Hi Assa,

The problem is that you've not provided the input files via the appropriate -1 and -2 flags. For your particular command, the command line should look like

$ salmon quant -p 16 --biasCorrect --libType IU -1 <(zcat ${base}_1.fastq.gz ) -2 <(zcat ${base}_2.fastq.gz) -i ~./Salmon/Salmon.index/Homo_sapiens.GRCh38.rel79/ --numBootstraps 100  -o $base 

Notice this looks almost the same as what you had before, except that the reads are prefixed by the relevant -1 and -2 flags, and come directly after the library type flags. Please let me know if this fixes the issue for you. I'll add a more informative message in such a situation.

from salmon.

thanks. Now it seems to work. I close this issue.

from salmon.