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Old 12-12-2019, 08:08 AM   #678
robinsleith
Junior Member
 
Location: Massachusetts

Join Date: Dec 2019
Posts: 1
Default Change in minid implementation?

Hello, I recently noticed that newer versions >=38.68 do not seem to implement minid in the same way as previous versions.

For the same command (same minid, 99), same reads, same reference, with versions <38.68 I get 0 mated pairs mapped, 4 Read 1 mapped, and 6 Read 2 mapped.

Code:
bbmap.sh nodisk minid=99 mappedonly=T threads=4 ref=parcu18S.fasta in=LKH421_FPE_q24_minlen100.fastq.gz in2=LKH421_RPE_q24_minlen100.fastq.gz out=stdout.sam | reformat.sh in=stdin.sam out=stdout.sam minlength=80 | samtools view -h -b -S | samtools sort >67_99parcu.bam
For versions >=38.68 I get 94 mated pairs mapped, 94 Read 1 reads mapped, and 94 Read 2 reads mapped.

Is the minid command just not working in newer versions or is there a new detail I am missing?
Thanks!
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