Hello,
I want to use the KEGG function of MEGAN6, but i can’t download the KEPP mapping files, it shows that Not Found.
I’ve tried this:
wget ftp://ftp.kegg.jp/pathway/genes/genes.keg
and got:
Resolving ftp.kegg.jp (ftp.kegg.jp)… 133.103.200.31
Connecting to ftp.kegg.jp (ftp.kegg.jp)|133.103.200.31|:21… connected.
Logging in as anonymous … Logged in!
==> SYST … done. ==> PWD … done.
==> TYPE I … done. ==> CWD (1) /pathway/genes …
No such directory ‘pathway/genes’.
We don’t host KEGG data directly. If you’re experiencing issues with KEGG, you may need to contact the KEGG developers. However, MEGAN provides KEGG mapping in the Ultimate Edition. To use this, you need to align your reads against the nr database, then use MEGAN’s mapping file to “meganize” your data. Once done, you can explore KEGG pathways within MEGAN.
If you wish to use custom KEGG data from the link you mentioned, you’ll need to have your own mapping file; otherwise, it won’t work. Alternatively, if you let me know exactly what you’re trying to do, I’d be happy to assist further—apologies if I’ve misunderstood your question.
Also, please use MEGAN 7(MEGAN7 Download ), as it’s the most up-to-date version.
We have some helpful resources for understanding DIAMOND + MEGAN analysis. Although they reference MEGAN 6, you can simply substitute MEGAN 7, and the instructions should still be applicable. Here are the links:
thank you for your reply, yes I meant Megan UE.
I’ve done blastx using diamond and got daa files, now I want to use megan to get the taxonomy and the gene function with kegg.
so i should run the kegg on the nr database like diamond ?
then how do i get this: acc2kegg-Jul2023X.bin
the cmd that i want to run is: PATH/megan/tools/daa2rma -i PATH/diamond_output/file.daa -o PATH/megan_output/output.rma -acc2tax PATH/megan/prot_acc2tax-Jul2023X.bin -acc2kegg PATH/megan/acc2kegg-Jul2023X.bin
please let me know if there’s a better way to do it,
You can then meganize this DAA file by using the MEGAN daa-meganizer tool:
daa-meganizer -i sample.daa -mdb megan-mapping.db
The mapping database (megan-mapping.db) contains classifications for taxonomy, KEGG, and more. MEGAN will analyze the alignments in the DAA file, find corresponding protein accessions in the mapping file (for taxonomy, KEGG pathways, etc.), and assign them to the reads using its algorithms.
Once the DAA file is processed, you can open it in MEGAN, click on the KEGG viewer, and analyze the required pathways, etc, and same you can do for taxonomy, and other classifications as needed.
If you are using the Ultimate Edition of MEGAN, make sure to use the corresponding Ultimate Edition mapping file from MEGAN DOWNLOAD PAGE, as it includes additional data for KEGG and other features.
Please note that the commands above are just a reference. Depending on your data (e.g., long vs. short reads), you may need to add additional flags to customize the process.