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nickloman.github.io
Hi Nick,
I have tried on the nanopore scripts but encounter some problems.
Hope you can give me some advice.
I have used your Ecoli nanopore-r9 2d data as the input.
When running bwa, I found this one line command doesn't work for me:
bwa mem -t8 -xont2d NC_000913.fna E_coli_K12_1D_R9.2_SpotON_2.pass.fasta | samtools view -bS - | samtools sort - -o E_coli_K12_1D_R9.2_SpotON_2.sorted.bam
So I have splited them as follow and though I don't actually know what the parameter -xont2d means and no space after -t?:
Everything seems fine for these steps, so I continue to run your nanopore script, expand-cigar.py:
python expand-cigar.py --bam R9_Ecoli_aln.sorted.bam --fasta NC_000913.fna > R9_Ecoli_aln.sorted.expanded.bam
There is no error return from expand-cigar, but when I run count-errors.py:
python count-errors.py R9_Ecoli_aln.sorted.expanded.bam
Error occured as:
Traceback (most recent all last):
File "count-errors.py", line 80, in
read_type = query.split('_')[4]
IndexError: list index out of range
Do you have any idea about this error? Is it due to no query in my best_align?
Thanks.
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