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Hi,
I used CRAQ to correct my genome assembly using short-reads, and I expected to get the CRAQ-corrected FASTA fragments since I used -b T.
The code was as followed:
perl /home/juaguila/app/CRAQ/bin/craq -g myse-hapog.fasta -ngs MYSE.Q20.mapped.sort.bam -D craq-myse-corr -t 12 -b T
I mapped the reads to the assembly, then filtered out those with low mapping quality, then bam converted, sorted, and indexed the bam file.
I checked the craq-myse-corr folder and I didn't find any out_correct.fa file.
Short-reads aren't enough for correcting the query fasta?
Thanks;
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