kaiju_mircea.md

Downloaded the trimmed, abundance filtered reads for the mircea data set. Ran kaiju as indicated below, using databases built here (https://gist.github.com/taylorreiter/2511b0c6e904b455e7002742c5da1492).

kaijudb -e

~/kaiju/bin/kaiju -t ~/kaijudb_e/nodes.dmp -f ~/kaijudb_e/kaiju_db_nr_euk.fmi -i SRR606249.pe.qc.fq.gz.abundtrim -v -o kaijudb_e_SRR606249.pe.qc.fq.gz.abundtrim.out

Then added taxonomy to kaiju names

~/kaiju/bin/addTaxonNames -t ~/kaijudb_e/nodes.dmp -n ~/kaijudb_e/names.dmp -i kaijudb_e_SRR606249.pe.qc.fq.gz.abundtrim.out -o kaijudb_e_SRR606249.pe.qc.fq.gz.abundtrim.out.names

Then made kaiju summary report

 ~/kaiju/bin/kaijuReport -t  ~/kaijudb_e/nodes.dmp -n  ~/kaijudb_e/names.dmp -i kaijudb_e_SRR606249.pe.qc.fq.gz.abundtrim.out -r genus -o kaijudb_e_SRR606249.pe.qc.fq.gz.abundtrim.out.summary


~/kaiju/bin/kaijuReport -t  ~/kaijudb_e/nodes.dmp -n  ~/kaijudb_e/names.dmp -i kaijudb_e_SRR606249.pe.qc.fq.gz.abundtrim.out -r species -o kaijudb_e_SRR606249.pe.qc.fq.gz.abundtrim.out.species.summary

Converted files to be krona compatible

~/kaiju/bin/kaiju2krona -t  ~/kaijudb_e/nodes.dmp -n ~/kaijudb_e/names.dmp -i kaijudb_e_SRR606249.pe.qc.fq.gz.abundtrim.out -o kaijudb_e_SRR606249.pe.qc.fq.gz.abundtrim.out.krona

Ran krona on kaiju output

ktImportText -o kaijudb_e_SRR606249.pe.qc.fq.gz.abundtrim.out.html kaijudb_e_SRR606249.pe.qc.fq.gz.abundtrim.out.krona

kaijudb -p

~/kaiju/bin/kaiju -t ~/kaijudb_p/nodes.dmp -f ~/kaijudb_p/kaiju_db.fmi -i SRR606249.pe.qc.fq.gz.abundtrim -o kaijudb_p_SRR606249.pe.qc.fq.gz.abundtrim.out

Then added taxonomy to kaiju names

~/kaiju/bin/addTaxonNames -t ~/kaijudb_p/nodes.dmp -n ~/kaijudb_p/names.dmp -i kaijudb_p_SRR606249.pe.qc.fq.gz.abundtrim.out -o kaijudb_p_SRR606249.pe.qc.fq.gz.abundtrim.out.names

Then made kaiju summary report

~/kaiju/bin/kaijuReport -t  ~/kaijudb_p/nodes.dmp -n  ~/kaijudb_p/names.dmp -i kaijudb_p_SRR606249.pe.qc.fq.gz.abundtrim.out -r genus -o kaijudb_p_SRR606249.pe.qc.fq.gz.abundtrim.out.summary

~/kaiju/bin/kaijuReport -t  ~/kaijudb_p/nodes.dmp -n  ~/kaijudb_p/names.dmp -i kaijudb_p_SRR606249.pe.qc.fq.gz.abundtrim.out -r genus -o kaijudb_p_SRR606249.pe.qc.fq.gz.abundtrim.out.species.summary

Converted files to be krona compatible

~/kaiju/bin/kaiju2krona -t  ~/kaijudb_p/nodes.dmp -n ~/kaijudb_p/names.dmp -i kaijudb_p_SRR606249.pe.qc.fq.gz.abundtrim.out -o kaijudb_p_SRR606249.pe.qc.fq.gz.abundtrim.out.krona

Ran krona on kaiju output

ktImportText -o kaijudb_p_SRR606249.pe.qc.fq.gz.abundtrim.out.krona.html kaijudb_p_SRR606249.pe.qc.fq.gz.abundtrim.out.krona

kaijudb -n

~/kaiju/bin/kaiju -t /mnt/work/kaijudb_n/nodes.dmp -f /mnt/work/kaijudb_n/kaiju_db_nr.fmi -i SRR606249.pe.qc.fq.gz.abundtrim -o kaijudb_n_SRR606249.pe.qc.fq.gz.abundtrim.out

Then added taxonomy to kaiju names

~/kaiju/bin/addTaxonNames -t /mnt/work/kaijudb_n/nodes.dmp -n /mnt/work/kaijudb_n/names.dmp -i kaijudb_n_SRR606249.pe.qc.fq.gz.abundtrim.out -o kaijudb_n_SRR606249.pe.qc.fq.gz.abundtrim.out.names

Then made kaiju summary report at genus level and species level

~/kaiju/bin/kaijuReport -t /mnt/work/kaijudb_n/nodes.dmp -n /mnt/work/kaijudb_n/names.dmp -i kaijudb_n_SRR606249.pe.qc.fq.gz.abundtrim.out -r genus -o kaijudb_n_SRR606249.pe.qc.fq.gz.abundtrim.out.summary

~/kaiju/bin/kaijuReport -t /mnt/work/kaijudb_n/nodes.dmp -n /mnt/work/kaijudb_n/names.dmp -i kaijudb_n_SRR606249.pe.qc.fq.gz.abundtrim.out -r species -o kaijudb_n_SRR606249.pe.qc.fq.gz.abundtrim.out.species.summary

Converted files to be krona compatible

~/kaiju/bin/kaiju2krona -t /mnt/work/kaijudb_n/nodes.dmp -n /mnt/work/kaijudb_n/names.dmp -i kaijudb_n_SRR606249.pe.qc.fq.gz.abundtrim.out -o kaijudb_n_SRR606249.pe.qc.fq.gz.abundtrim.out.krona

Ran krona on kaiju output

ktImportText -o kaijudb_n_SRR606249.pe.qc.fq.gz.abundtrim.out.krona.html kaijudb_n_SRR606249.pe.qc.fq.gz.abundtrim.out.krona

kaijudb -r

~/kaiju/bin/kaiju -t /mnt/work/kaijudb_r/nodes.dmp -f /mnt/work/kaijudb_r/kaiju_db.fmi -i SRR606249.pe.qc.fq.gz.abundtrim -o kaijudb_r_SRR606249.pe.qc.fq.gz.abundtrim.out

Then added taxonomy to kaiju names

~/kaiju/bin/addTaxonNames -t /mnt/work/kaijudb_r/nodes.dmp -n /mnt/work/kaijudb_r/names.dmp -i kaijudb_r_SRR606249.pe.qc.fq.gz.abundtrim.out -o kaijudb_r_SRR606249.pe.qc.fq.gz.abundtrim.out.names

Then made kaiju summary report at genus level

~/kaiju/bin/kaijuReport -t /mnt/work/kaijudb_r/nodes.dmp -n /mnt/work/kaijudb_r/names.dmp -i kaijudb_r_SRR606249.pe.qc.fq.gz.abundtrim.out -r genus -o kaijudb_r_SRR606249.pe.qc.fq.gz.abundtrim.out.summary

~/kaiju/bin/kaijuReport -t /mnt/work/kaijudb_r/nodes.dmp -n /mnt/work/kaijudb_r/names.dmp -i kaijudb_r_SRR606249.pe.qc.fq.gz.abundtrim.out -r species -o kaijudb_r_SRR606249.pe.qc.fq.gz.abundtrim.out.species_summary

Converted files to be krona compatible

~/kaiju/bin/kaiju2krona -t  /mnt/work/kaijudb_r/nodes.dmp -n /mnt/work/kaijudb_r/names.dmp -i kaijudb_r_SRR606249.pe.qc.fq.gz.abundtrim.out -o kaijudb_r_SRR606249.pe.qc.fq.gz.abundtrim.out.krona

Ran krona on kaiju output

ktImportText -o kaijudb_r_SRR606249.pe.qc.fq.gz.abundtrim.out.krona.html kaijudb_r_SRR606249.pe.qc.fq.gz.abundtrim.out.krona