You can run BBMap like this:
Code:
bbmap.sh in=reads.fq outm=normal.bam outu=unmapped.fq pairedonly ambig=all maxindel=400k
Code:
bbmap.sh in=unmapped.fq out=odd.bam ambig=all local maxindel=400k
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bbmap.sh in=reads.fq outm=normal.bam outu=unmapped.fq pairedonly ambig=all maxindel=400k
bbmap.sh in=unmapped.fq out=odd.bam ambig=all local maxindel=400k
bbmap.sh in=raw_reads.fastq.gz outu=stdout.sam qin=auto qout=33 qtrim=lr maq=30 mintrimlength=30
1600:7:1:1413:2208 653 * 0 0 * * 0 0 AAATGAAGAGAAAGATTACAGGGAAGTAAC ##############################
bbmap.sh in1=reads_R1.fq in2=reads_R2.fq ref=scaffolds.fasta nodisk covstats=stats.txt covhist=histogram.txt
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