Hello,
I have tried to run sga-bam2de.pl a few times with bowtie sorted bam files. I changed the samtools bit by adding -o and .bam at the end to make it compatible with newer versions of samtools and I get .hist files and .diffcontigs.sorted.bam which appear ok but the de file is empty.
I've also tried to run DistanceEst with the same setting abyss used in the assembly I got the bam file and got the same output.
Hello, I have tried to run sga-bam2de.pl a few times with bowtie sorted bam files. I changed the samtools bit by adding -o and .bam at the end to make it compatible with newer versions of samtools and I get .hist files and .diffcontigs.sorted.bam which appear ok but the de file is empty. I've also tried to run DistanceEst with the same setting abyss used in the assembly I got the bam file and got the same output.
Here are a couple of DistanceEst tries I had: DistanceEst -s 1000 --mind -99 -n 5 -k 64 -j 1 -o output.de input.hist -l 200 input.diffcontigs.sorted.bam DistanceEst -s 200 --mind 63 -n 5 -k 64 -j 10 -o output.de input.hist -l 200 input..diffcontigs.sorted.bam DistanceEst -s 200 --mind 63 -n 5 -k 64 -j 10 -l 200 -o output.de input.hist input.diffcontigs.sorted.bam Any advice?