search

mourisl / Rcorrector

Error correction for Illumina RNA-seq reads
GNU General Public License v3.0
62 stars 18 forks source link

Running jellyfish2 #21

Closed 000generic closed 4 years ago

000generic commented 4 years ago

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!

mourisl commented 4 years ago

You should run rcorrector through the wrapper "perl run_rcorrector.pl". Jellyfish and other parts are all handled there.

000generic commented 4 years ago

Works great! Thank you for such a quick response :) Eric