BOL: Results for "Mers"

Results for "Mers"

- Jit@jit.aber
Clump Finding Problem Solved with Perl
...ven: A string Genome, and integers k, L, and t. #Return: All distinct k-mers forming (L, t)-clumps in Geno...($string, $subStr, $kmer); sub kmerMatch { #Check the exact matching kmers with sliding window my ($str...
2347 days ago
- Rahul Nayak@rahul
Estimate Genome Size
# Count k-mer occurrence using Jellyfish 2.2.6 jellyfish count -t 8 -C -m 19 -s 5G -o 19mer_out --min-qual-char=? sread_1.fastq sread_2.fastq # points for a histogram jellyfish histo -o 19mer_out.histo 19mer_out #Plot results using R ##load the data into dataframe19 dataframe19
2277 days ago
- Jit@jit.aber
Running Trinity on RNA-seq !
...D: jellyfish histo -t 40 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf CMD f...h dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa CMD finished (16 seconds)...jellyfish dump -L 1 mer_counts.jf > jellyfish.kmers.fa * Running CMD: jellyfish...
2140 days ago
- Jit@jit.aber
Downloading GATK !
...ls that perform metagenomic analysis, e.g. microbial community composition and pathogen detection PathSeqBuildKmers Builds set of host reference k-mers PathSeqBuildReferenceTax...
2088 days ago
- Rahul Nayak@rahul
Plot kmer stats in bash !
#!/bin/bash #Counting k-mers for different k echo "k,unique,distinct,total" for k in {1..15}; do kat hist -o phiX_$k.hist -m $k phiX.fasta >/dev/null 2>&1 egrep -v '^#' phiX_$k.hist|awk '{if ($1==1) u=$2; d+=$2; t+=$2*$1;}\ END{print "'$k',"u","d","t}' done
807 days ago