Hello everyone, I get very low mapping ratio using bowtie2 like this , what can I do?
Low mapping rates can usually be addressed by these:
- Do some QA/QC on the reads before mapping
- Double check that the reads are from the same species as the target reference genome
- If reference annotation is incorporated, it must match the reference genome (version/build)
- Check that the read orientation is a match for the settings specified on the mapping tool form.
- Try using the most current tool appropriate for the analysis step. In this case,
HISAT2is the replacement for
Bowtie2(mapping RNA-seq reads).
GTN Tutorials for “Transcriptomics”. Most of the above are covered. Galaxy Training!
You can also search this forum or the tutorial site with keywords like: mapping, hisat2, qa-qc, transcriptomics, gtf