Difference in mapping rate when aligned with mapper.pl of miReep2 and bowtie1

Question

[MIKA]

I performed alignment using the same small RNASeq data and reference genome using miRDeep2 and bowtie1, respectively. It is known that miRDeep2 uses bowtie1 for mapping, but the results using miRDeep2 and the results using bowtie1 show very different mapping rates.

While approximately 20% of the results for miRDeep2 are mapped, 85% of the results for bowtie1 are mapped.

The options used are as follows.

• miRDeep2

  mapper.pl 2023.fastq -e -h -i -j -m -p /home/song/miRNAseq/bowtie_index/STAR/index -s collapsed_2023.fa -t genome_after_2023.arf -v -o 1

• bowtie1

  bowtie -v 1 -p 4 -S /home/song/miRNAseq/bowtie_index/STAR/index 2023.fastq > ./hg38/38_aligned_data.sam

What's the difference?

I am curious about how to increase the mapping rate when using miRDeep2 and how to analyze the level of miRNA expression using the sam file, which is the result file of bowtie.

Answer 1

[wessel.willemsen]

I had the same problem as you but i solved it by allowing the reads to map to more targets. By default mapper.pl does not allow a read to map to more than 5 places. You can solve this by setting -r to 100 in the mapper.pl command. Hope this helps!