Help! I'm trying to use DSK k mer counting software and GCE to estimate genomic characters
1
0
Entering edit mode
10.4 years ago
ab.tsubaki ▴ 50

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!

kmer genome-size next-gen • 2.9k views
ADD COMMENT
0
Entering edit mode
10.3 years ago
Rayan Chikhi ★ 1.5k

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.

ADD COMMENT
0
Entering edit mode

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!

ADD REPLY
0
Entering edit mode

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!

ADD REPLY

Login before adding your answer.

Traffic: 1754 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6