I have mapped fastq files to my transcriptome of interest in Kallisto, and performed a differential expression analysis in Sleuth (control versus sample). Although I obtain a list of differentially expressed loci after performing a Wald test, a look at the read mapping metrics makes me unsure about the data. The mappings I obtain are as follows:
sample reads_mapped reads_proc frac_mapped bootstraps control_replicate1 39333462 48943096 0.8037 100 control_replicate2 41571482 51237738 0.8113 100 sample_replicate1 15284000 21768028 0.7021 100 sample_replicate2 9515367 21270730 0.4473 100
As you can see, sample_replicate2 is considerably fewer reads mapped than the other sample and controls. Will this impact my differential analysis. Since they are scale in sleuth (i.e. sleuth normalised tpm) will this be an issue?