Results for "Graph-theory based studies"
Bio-Scripts
Extracting FASTA sequences based on position with perl script !!
#!/usr/bin/env perl #Uses: perl sub-seq.pl input.txt range use strict; use warnings; my $end = pop; my $start = pop; local $/ = '>'; while () {...2651 days ago
- # 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
2294 days ago
Estimate Genome Size with Jellyfish and R
jellyfish count -t 8 -C -m 19 -s 5G -o 19mer_out --min-qual-char=? /common/Tutorial/Genome_estimation/sample_read_1.fastq /common/Tutorial/Genome_estimation/sample_read...2276 days ago
- ➜ trinityrnaseq-Trinity-v2.6.6 git:(master) ✗ ./Trinity --seqType fq --max_memory 250G --left /media/urbe/MyPassp...during normalization. 0 / 16641634 = 0.00% reads discarded as likely aberrant based o...
2157 days ago
- ➜ bin git:(master) ✗ ./fastq-dump --help Usage: ./fastq-dump [options] [...]...ilter used in current 1000 Genomes data Filters based on alignments Filters..."chr1" or "1"). "from" and "to" are 1-based...
2156 days ago
- ➜ BorisTrinityAssembly /home/urbe/Tools/transrate-1.0.3-linux-x86_64/transrate _...ranscriptome assembly using three kinds of metrics: 1. sequence based (if --assembly is given) 2. read mapping based (...
2153 days ago
Installing Porechop on Ubuntu !
➜ Tools git:(master) ✗ git clone https://github.com/rrwick/Porechop.git Cloning into...he format will be chosen based on the output filename or the...e binning settings: Control the binning of reads based o...2136 days ago
- jitendra@jitendra-UNLOCK-INSTALL[SNP] wget https://github.com/broadinstit...(Picard) Creates a hash code based on the read groups (RG)....from a SAM or BAM file. CollectBaseDistributionByCycle (Picard)...es into a single file. PositionBasedDo...
2105 days ago
Bash script to alignment of short reads against reference genome !
bwa mem -t 40 -R '@RG\tID:K12\tSM:K12' \ E.coli_K12_MG1655.fa SRR1770413_1.fastq.gz SRR1770413_2.fastq.gz \...RR1770413.bam --- this marks reads which appear to be redundant PCR duplicates based o...1589 days ago
Installing ggplot2 and its dependencies on Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads/MitoHunter/minidot/bin$ sudo R [sudo] password for jit: R version 3.4.4 (2...ed CPPFLAGS, LDFLAGS, and LIBS... done checking whether we may build an ICU4C-based p...1580 days ago
