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

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

3.9 years ago by

ab.tsubaki • 30

South Africa

ab.tsubaki • 30 wrote:

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 (http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/gce/README.txt.htm 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!

genome size k mer next-gen • 1.4k views

ADD COMMENT • link •

modified 3.8 years ago by Rayan Chikhi • 1.3k • written 3.9 years ago by ab.tsubaki • 30

3.8 years ago by

Rayan Chikhi • 1.3k

France, Lille, CNRS

Rayan Chikhi • 1.3k wrote:

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 • link modified 3.8 years ago • written 3.8 years ago by Rayan Chikhi • 1.3k

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 • link written 3.3 years ago by Maryam • 0

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 • link modified 3.3 years ago • written 3.3 years ago by Rayan Chikhi • 1.3k

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