create a test set

[beebee0]

Hello,
Can you please describe the set of commands and include the intermediate BAM/SAM file along with DB file? A test set of commands and output would be really useful. I'm using bowtie2 and getting errors unable to plot. The database creation I can't tell if is the problem (it creates the file, exit status 0) or if it's the plotting that's the issue.

I formed the SAM from bowtie2 --no-unal --no-mixed --no-discordant -X 1000 -x $idx -1 $R1 -2 $R2 | samtools view -bS | samtools sort -o sorted.bam && samtools view -h -o out.sam sorted.bam Then I ran rpe build --genome $assembly --reads out.sam --database db

I get a 80K db file from a 13G SAM input file and unsure what the DB file contains to know if that's right or not.

Thank you!