Hopefully someone can help. I have read conflicting info about aligners for miRNA data but I have finally decided on Bowtie2. I have 3 questions:
1. Can anyone share the parameters they are using to run Bowtie2 to align miRNA and give a short explanation for the choices?
2. I am aligning to the human genome and then using HTSeq with the gff file from miRBase to count the miRNAs aligned in the BAM file, is this a reasonable approach?
3. Does anyone know if HTSeq will accurately count miRNAs that map to multiple locations in the genome?
Thanks everyone!
1. Can anyone share the parameters they are using to run Bowtie2 to align miRNA and give a short explanation for the choices?
2. I am aligning to the human genome and then using HTSeq with the gff file from miRBase to count the miRNAs aligned in the BAM file, is this a reasonable approach?
3. Does anyone know if HTSeq will accurately count miRNAs that map to multiple locations in the genome?
Thanks everyone!
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