A single read 50 RNA-seq experiment (NEB, riboZero) was used to compare diffential expression with 3 strategies: HtSeq-count-gene (union, version 0.6.1p1), salmon-gene (version : 0.4.0, --libType SR --unmatedReads --extraSensitive --biasCorrect, but the bias corrected file was not used) and kallisto-gene (kallisto 0.42.1). The reads were aligned to mm10 using star-aligner. Ensembl GRCh38 78 gtf was used as annotation. For salmon (non bias corrected) and kallisto the indices were generated from Homo_sapiens.GRCh38.cdna.all.fa.gz and Homo_sapiens.GRCh38.ncrna.fa.gz. The experiment consisted of 4 conditions with 2 replicates each. Gene counts were derived from kallisto with a home made script by summing estimated counts/transcripts per gene. Differential expression was called using DESeq2.
Only the comparison for one condition is shown. The other conditions had similar results regarding htseq/kallisto/salmon.
The bottom line is that the differences are neglegible.
Alignment statistics show a nice stranded undegraded preparation
Scatter plots show high correlation between the different methods. Numbers are spearman correlation of plotted values.