Open SimonHegele opened 8 months ago
I believe your command is incorrect. It should be
kraken2 --db {database} --report {report} --threads {threads} --paired {query} {mate} > {out} 2> {log}
Read files should be given last. and do not need to be right after the --paired argument
Tried to classify samples from paired-end sequencing using the command:
kraken2 --db {database} --paired {query} {mate} --report {report} --threads {threads} > {out} 2> {log}
My samples had 60-80 million read pairs, however Kraken2 reported 120-160 million fragments (two times as much). Apparently each read is counted. At the same time same taxa have uneven numbers of associated fragments. This indicates that the reads of a read pair could be mapped to different taxa.