Help! I'm trying to use DSK k mer counting software and GCE to estimate genomic characters

Question

[ab.tsubaki]

Hi all

Can ANYONE please point me in the right direction for help with DSK and GCE?

I have been able to successfully run DSK but I don't know what to do with the binary output files???

I have found some info on GCE as well as the GCE manual but I have no idea how to start running it? My main concern is the kmer_depth_file: is this something I need to create because it's not inside the GCE package? It also provides you with two different scripts as shown below:

gce -f test.freq [-g total_kmer_num]
./gce -f kmer_depth_file >gce.table 2>gce.log ##basic standard discrete model.

What do each of these do and which one is used for the actual run? Where do I give it my input files???

Anyone with some experience in using these software packages, please point me in the right direction?

Thanks!

Answer 1

[Rayan Chikhi]

Hi! Your question wasn't tagged DSK so I didn't see it immediately..

The DSK binary file can be viewed (in a natural format, [kmer] [abundance]), using the parse_results program provided with DSK. You can follow the indications in the README.

[Maryam]

Hello. I tried visualizing the DSK output binary file as suggested in the README, using 'parse_results'. However, I got:

The solid k-mers file was created with make k=2043402102 but this software was compiled with make k=32

The command I used to run DSK was:

./dsk myfile.fasta 32 -o out_dsk -histo -c

Do you have any idea of what the message means? Or how can I solve it?

Thank you!

[Rayan Chikhi]

Hi!

The reason you're getting this error is because parse_results does not work when the -c option is specified. Please re-run DSK without -c and it will work!