Bowtie2 mapping rate low

Hello everyone, I get very low mapping ratio using bowtie2 like this , what can I do?
Thank you!

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Hi @Yuliang_Wang

Low mapping rates can usually be addressed by these:

  1. Do some QA/QC on the reads before mapping
  2. Double check that the reads are from the same species as the target reference genome
  3. If reference annotation is incorporated, it must match the reference genome (version/build)
  4. Check that the read orientation is a match for the settings specified on the mapping tool form.
  5. Try using the most current tool appropriate for the analysis step. In this case, HISAT2 is 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