search

YeoLab / MINES

(m)6A (I)dentification Using (N)anopor(E) (S)equencing
18 stars 3 forks source link

FASTA file format #3

Open ceslobfer opened 4 years ago

ceslobfer commented 4 years ago

Hi. I am trying to use MINES but I get the following error:

WARNING. chromosome (pp_24194) was not found in the FASTA file. Skipping.

I don't know if this is because the sequences in fasta format must have a certain format. My reference FASTA has the following format:

pp_id ATGC ...

ceslobfer commented 4 years ago

Also when I launch the cDNA example command but with my data: python cDNA_MINES.py --fraction_modified output_filename.fraction_modified_reads.plus.wig.bed --coverage output_filename.coverage.plus.bedgraph --output m6A_output_filename.bed --ref REF.fa

It gives me the following error:

cDNA_MINES.py: error: argument --kmer_models is required

I assumed it was:

python cDNA_MINES.py --fraction_modified output_filename.fraction_modified_reads.plus.wig.bed --coverage output_filename.coverage.plus.bedgraph --output m6A_output_filename.bed --ref REF.fa --kmer_models Final_Models /

aman21392 commented 4 years ago

can you please tell me you successfully run this pipeline or not because i also run this i got some error.