Am working on mapping some Nanopore RNA reads to rat reference. I have been using minimap2 and guppy_aligner to try and accomplish this, but have unfortunately had many errors with both programs. One I am wondering is the Parse error in the SAM file that is output from:
./guppy_aligner -I <input/path/ (.fastq)> -s <output/path/ (.sam)> --align_ref ./Rat/NCBI_Transcriptome/GCF_015227675.2_mRatBN7.2_rna.fa --align_type auto
Can anyone enlighten me as to why I am getting this error? I have also used the transcriptome .fa file from NCBI and get a similar error, where the first non-header line output of
samtools view -h <output.sam> is not parseable.
Also, if you happen to know which rat reference file to use with minimap2 or guppy aligner, alongside the settings you use, that would be the best headache relief medicine.