I am trying to use miRDeep2 to identify known or novel miRNAs from deep sequencing data. I already trimmed my data using TrimGalore and aligned using Bowtie, and converted sam to bam using Samtools. However, miRDeep2.pl takes mapped reads to the genome in miRDeep2 ARF format, which means that I need to convert sam files to ARF format using
bwa_sam_converter.pl. When I try to run the
bwa_sam_converter.pl code, I always got Arf file not found error but it needs to be output of the code. Please find my usage in below:
perl /.../bwa_sam_converter.pl /.../X.sam reads.fa reads_vs_genome.arf
I would appreciate if someone can help me.