miRDeep2 and adapter trimming

[Anastaziel]

I am trying to align a miRNA-seq FASTQ file using the mapper.pl from miRDeep2 but I am not having any luck.

The reads in the FASTQ file are ~50bp.

I am not sure where my mistake is as I get 46380 reads mapped (less than 1.6% of total reads). This is my code

mapper.pl /mnt/d/work/NNNN_1_SAMPLE1_ATCACGA_S2_L001_R1_001.fastq -e -h -j -k ATCACGA -l 16 -m -p GRCh38_primary_assembly_genome -s /mnt/d/work/tools/mirdeep2/test/2.collapsed_reads.fa -
t /mnt/d/work/tools/mirdeep2/test/2.grch38.arf -n -v

I think my mistake is with the adapter sequence. The adapter for this sample is ATCACGA (it is in the sample name too). I looked at this website illumina-adapter-and-primer-sequences/ and my samples (I do have more) follow the TruSeq™ DNA Sample Prep Kit v2 but if I try to put a longer adapter (TruSeq Adapter, Index 1) I just get +- 10000 mapped reads.

I am not sure how to proceed. Any help would be appreciated.

[Anastaziel]

I think I fixed it. The adapter for my files should be TGGAATTCTCGGGTGCCAAGG. From what-sequences-do-i-use-for-adapter-trimming under the category of TruSeq Small RNA.

Now I get ~60% mapping. I am not sure if this is sufficient, though.