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mor rubinstein
Mar 12, 2013, 9:47:35 AM3/12/13
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Dear all,
Please help me as I found no reference to this topic in the discussions here or anywhere else. (googled it).
I want to build the DBG and discard the low cover k-mers from it. I first ran SOAPdenovo pregraph to get the kmer cover distribution from the .kmerFreq file and decide what cutoff to use, and then ran pregraph again with the -d option. My command was:
Please help me as I found no reference to this topic in the discussions here or anywhere else. (googled it).
I want to build the DBG and discard the low cover k-mers from it. I first ran SOAPdenovo pregraph to get the kmer cover distribution from the .kmerFreq file and decide what cutoff to use, and then ran pregraph again with the -d option. My command was:
SOAPdenovo pregraph -s seqreads.config -p 30 -K 21 -o k21 -d 12 -R &
when I looked at the .kmerFreq file created this time, indeed all kmers with cover 12 or less got a value of 0, except kmers with cover or 1 - their frequency did not change at all. Does it mean that kmers with frequency of 1 were left in the graph? Is this a bug or is there a reason for that?
Thanks,
Mor
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