miRDeep2 - identifying miRNAs from deep sequencing data

Question

[Hasan]

Hi there,

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.

Thanks

Answer 1

[bk11]

You need to provide flags (i/c/o/a)-

perl bwa_sam_converter.pl -i X.sam -c -o reads.fa -a reads_vs_genome.arf

If read ids are already collapsed and in correct miRDeep2 format (eg. ">ABC_1_x10", see file formats) then the sam file just needs to be converted:

perl bwa_sam_converter.pl -i X.sam -a reads_vs_genome.arf

[Hasan]

I tried with the flags too but still got the same error.

First 10 line of my sam file is as follows:

@HD VN:1.0  SO:unsorted
@SQ SN:chr1 LN:248956422
@SQ SN:chr2 LN:242193529
@SQ SN:chr3 LN:198295559
@SQ SN:chr4 LN:190214555
@SQ SN:chr5 LN:181538259
@SQ SN:chr6 LN:170805979
@SQ SN:chr7 LN:159345973
@SQ SN:chr8 LN:145138636
@SQ SN:chr9 LN:138394717

[Hasan]

Now I got this error: Sam file /.../1192.sam not found. However its indeed in the given path