I am trying to run miRDeep2 for the differential expression of miRNA in my dataset. I ran the mapper.pl without much hassle. However, I can't get the miRDeep2.pl to run and keep getting errors:
Here's the error that I am getting:
Error: problem with /data/lab/Homo_sapiens/Ensembl/GRCh37/Sequence/BowtieIndex/new_genome.fa
Error in line 9.221.351: The sequence
contains characters others than [acgtnACGTN]
Please check your file for the following issues:
I. Sequences are allowed only to comprise characters [ACGTNacgtn].
II. Identifiers are not allowed to have withespaces.
I got the error before for a nucleotide M in another sequence within the genome.fa file. I replaced it with N manually. However, it's showing me error with another sequence. Is there a way to get around this? Maybe I am missing something. Any help is appreciated.
Here's my command that I used to run the program:
miRDeep2.pl ABC.clipped_collapsed.fa /data/lab/Homo_sapiens/Ensembl/GRCh37/Sequence/BowtieIndex/new_genome.fa ABC.clipped_collapsed.arf /data/lab/Homo_sapiens/Ensembl/GRCh37/Annotation/SmallRNA/new_mature.fa none /data/lab/Homo_sapiens/Ensembl/GRCh37/Annotation/SmallRNA/new_precursor.fa