Running jellyfish2
Closed this issue · 2 comments
In contrast to Rcorrector GitHub directions, Rcorrector usage info at the command line seems to indicate I should first run Jellyfish2 on my reads (-c parameter).
Usage: ./rcorrector [OPTIONS]
OPTIONS:
Required parameters:
-r seq_file: seq_file is the path to the sequence file. Can use multiple -r to specifiy multiple sequence files
-p seq_file_left seq_file_right: the paths to the paired-end data set. Can use multiple -p to specifiy multiple sequence files
-i seq_file: seq_file is the path to the interleaved mate-pair sequence file. Can use multiple -i
-c jf_dump: the kmer counts dumped by JellyFish
-k kmer_length
If this is correct, do you have an example of command line settings I might use to run Jellyfish2? Also, is there a suggested method for determining the value to provide for -k ?
Thank you!
You should run rcorrector through the wrapper "perl run_rcorrector.pl". Jellyfish and other parts are all handled there.
Works great! Thank you for such a quick response :)
Eric