Thanks for Tsunglin and Tomas Flouri.
They reconnected the S.aureus with FLASH and COPE and found that they could not get the results shown in paper.
Here I show the details we used for the paper:
For the data of S. aureus, we directly used the Quake corrected reads in the published dataset.(Staphylococcus/Data/quakeCor/frag_*.fastq ).
The command for kmer freq: kmerfreq -l fq.list -q 33 -t 10 2>freq.log
The command for COPE: cope -a frag_1.fastq -b frag_2.fastq -o connect.fq -2 left1.fq -3 left2.fq -t freq.cz -f freq.cz.len -s 33 -m 3 >cope.log 2>cope.err
It is necessary to mention that -s 33 is essential for this dataset.
Best Regards, Binghang
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Thanks for Tsunglin and Tomas Flouri.
They reconnected the S.aureus with FLASH and COPE and found that they could not get the results shown in paper.
Here I show the details we used for the paper:
For the data of S. aureus, we directly used the Quake corrected reads in the published dataset.(Staphylococcus/Data/quakeCor/frag_*.fastq ).
The command for kmer freq:
kmerfreq -l fq.list -q 33 -t 10 2>freq.log
The command for COPE:
cope -a frag_1.fastq -b frag_2.fastq -o connect.fq -2 left1.fq -3 left2.fq -t freq.cz -f freq.cz.len -s 33 -m 3 >cope.log 2>cope.err
It is necessary to mention that -s 33 is essential for this dataset.
Best Regards,
Binghang
Last edit: Binghang Liu 2013-04-18