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!
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.bamThen I ranrpe build --genome $assembly --reads out.sam --database dbI 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!