jkwaldman

Just checked - the version I used was 1.2, so it shouldn't be returning unaligned reads already. @pcantalupo - The -no-unaligned option will cause an error if the user is...

@pcantalupo What was the command you used with samtools fastq for v1.5 that dropped the duplicate reads? Trying to replicate (having to use magicblast v1.2, which may be affecting things)...

@pcantalupo If you execute this line of code (from magicblast_w_opts.sh) with Samtools 1.5, it produces the proper fastq file? samtools fastq $out.bam -v 40 > $out_file -- MB 1.2 should...