generation of a log file? about chopper HOT 6 CLOSED

Hi Wouter, Thank you for the information about -c and for working towards the read removal log file! Thank you for sharing your programs. Brittany Brittany D. Cronk (she/they) Cornell University Animal Health Diagnostic Center Virology Laboratory ***@***.******@***.***> (607)253-4342

Hi Wouter, Thank you for the update! I hope you don't mind me troubleshooting further with you. I updated chopper from 0.2.0 to 0.4.0 by re-installing using conda -c bioconda install chopper, however I am not sure if it is working correctly. When I filtered for quality and removed host reads, i kept more reads then when I ran filtering for quality alone. This should ideally be the other way around. Am I doing something wrong with my command? I see you wrote zcat in your previous email, but it seems to work the same regardless as to when I use gunzip or zcat. gunzip -c ${samplename}.fastq.gz | chopper -q 10 -c /workdir/host_genomes/GCF_002263795.1_Bos_taurus_genomic.fna.gz 2> chopper.log | gzip > ${samplename}_filt.fastq.gz the chopper.log file just read: Kept 214706 reads out of 214897 reads vs zcat -c ${samplename}.fastq.gz | chopper -q 10 2> chopper4.log| gzip > ${samplename}_filt_test3.fastq.gz chopper4 file reads the same Kept 186136 reads out of 214897 reads I also ran it with the host again, after gunzip'ing the host file to see if that would make a different but the final result was still 214706 reads kept. Thanks, Brittany