Open danshu opened 7 years ago
Hi,
I'm using MaSuRCA and there is a genome size estimation step using jellyfish: log Estimating genome size. jellyfish count -m 31 -t 30 -C -s $JF_SIZE -o k_u_hash_0 pe.cor.fa export ESTIMATED_GENOME_SIZE=jellyfish histo -t 30 -h 1 k_u_hash_0 | tail -n 1 |awk '{print $2}' save ESTIMATED_GENOME_SIZE echo "Estimated genome size: $ESTIMATED_GENOME_SIZE" (commands in the assemble.sh file)
jellyfish histo -t 30 -h 1 k_u_hash_0 | tail -n 1 |awk '{print $2}'
I'm confused because this should be total number of 31-mers instead of genome size according to my understanding.
Best, Danshu
Hi,
I'm using MaSuRCA and there is a genome size estimation step using jellyfish: log Estimating genome size. jellyfish count -m 31 -t 30 -C -s $JF_SIZE -o k_u_hash_0 pe.cor.fa export ESTIMATED_GENOME_SIZE=
jellyfish histo -t 30 -h 1 k_u_hash_0 | tail -n 1 |awk '{print $2}'save ESTIMATED_GENOME_SIZE echo "Estimated genome size: $ESTIMATED_GENOME_SIZE" (commands in the assemble.sh file)I'm confused because this should be total number of 31-mers instead of genome size according to my understanding.
Best, Danshu