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!
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written
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ab.tsubaki •
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.
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written
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Rayan Chikhi
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!
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!
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written
by
Rayan Chikhi
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