newbie, do I need to re-run if paired ends argument are backwards -1 xyz.2.fastq -2 xyz_1.fastq

[Andy Davidson]

I just completed a very large run. While reviewing the output and the pipeline code that calls salmon I notice that the order of the paired reads was incorrect.

salmon produced quant.sf files. Are they any good or do I need to re-run everything? It will probably take a couple of weeks to re-run

My guess is if the files are backward Salmon will treat the files as if they are single-end reads. The result is the mapping will not be very accurate.

https://salmon.readthedocs.io/en/latest/salmon.html#providing-multiple-read-files-to-salmon
"' The left and right reads for lib_1 are lib_1_1.fq and lib_1_2.fq' "

```
         salmon quant \
              -i $refIndexDir \
              --libType A \
              -1 "${rightReads}" \
              -2 "${leftReads}" \
              -p $numThr \
              --recoverOrphans \
              --validateMappings \
              --gcBias \
              --seqBias \
              --rangeFactorizationBins 4 \
              --writeUnmappedNames \
            --output ${outDir}
```
Kind regards

Andy