I recently mapped and quantified my raw single cell RNA-seq reads using Salmon and found that many samples had low mapping rates (around 30 and 40 percent), so I'd like to evaluate the mapping results and see what happened.
RSeQC seems like a good tool for this, able to generate many metrics about the mapping. Unfortunately, it seems like RSeQC only takes BAM/SAM files, whereas I have quant.sf and other output files from Salmon.
Is there a way to make RSeQC work with the Salmon output files, and if not, what are some other mapping QC packages that work with Salmon?
I've tried searching but had trouble finding any.
Or will I have to re-run the alignment with a traditional aligner like STAR, and quantify, and use RSeQC? (More of a last resort option. I have thousands of fastq files and it took Salmon 28 hours to process all of them, so I'd like to avoid additional alignment if possible).
Which kind of scRNA-seq data are this? There might be specialized tools for it. Can you give some details?
The platform used was Illumina Smart-Seq2. I aligned with Salmon to the hg38 transcriptome using decoy sequences. I don't know if these are the details you are asking for. Let me know what else you need to know. Thanks.