Results for "NGS data analysis"
Bio-Scripts
➜ BorisTrinityAssembly /home/urbe/Tools/transrate-1.0.3-linux-x86_64/transrate...embly/transrateSTAT/Trinity/contigs.csv [ INFO] 2018-07-13 14:54:40 : Writing analysis results to assemblies.csv2115 days ago
- # list sample names & download URLs. sample_links = {"ERR458493": "https://osf.io/5da...LES=sample_links.keys() # download yeast rna-seq data from Schurch et al, 2016 stud...wnload_all: input: expand("rnaseq/raw_data/{sa...
1508 days ago
- set -e echo "Running reapr version 1.0.18 pipeline:" echo "/home/urbe/Tools/Reapr_1....adinetaGapFilled.gapfilled.iteration1.fa /home/urbe/DATA/OriginalReads/ANature/GC02756...26.HiSeq2000.FCB.lane1.gcap_dev.R1.fastq /home/urbe/DATA/Ori...
2091 days ago
Perl script to find palindromic pattern !
#!/usr/bin/perl use strict; use warnings; use strict; my %invert; @invert{ qw[ A C G T ] } = qw[ T G C A ]; my $in...substr( $in, $p1-$pals, ($pals+1)*2 ), $p1-$pals; } } __DATA__...2091 days ago
- ...------------------- Coverage Analysis:...Checks that all data in the input files appear to have...ools that perform metagenomic analysis, e.g. microbial community com...concordance between genotype data of one samples in each of two VCF...
2067 days ago
- ➜ upgrade_oh_my_zsh Updating Oh My Zsh remote: Counting objects: 484, done. remote: Compressing objects: 100%...emoji/README.md | 6 +- plugins/emoji/emoji-data.txt...
2067 days ago
Installing pb-assembly on Linux !
[jnarayan@hmem00 ~]$ module avai...ssembly Fetching package metadata ........... Solving package...all bwa Fetching package metadata ............. Solving packag...e currently available SMRT(R) Analysis builds. While # # efforts ha...e currently available SMRT(R) Analysis builds. While # # efforts ha...2026 days ago
- (denovo_asm) [jnarayan@hmem00 ~]$ git clone https://github.com/cdunn2001/git-sym.git fatal: destination path 'gi...-sym.makefile 'greg200k-sv2.2' curl -L https://downloads.pacbcloud.com/public/data/git...
2026 days ago
- #! /usr/bin/Rscript ## Collect arguments args
1996 days ago
CollectGcBiasMetrics.jar will generate a GC bias plot for each contig
samtools index aln-pe.mapped.sorted.bam for i in $(samtools view -H aln-pe.mapped.sorted.bam | awk -F"\t" '/@S...-pe.mapped.sorted.$i.bam; java -Xmx2g -jar $(which CollectGcBiasMetrics.jar) R=data/Cdi...1996 days ago
