Results for "single-molecule physical genome mapping"
Bio-Scripts
Perl subroutine to read genome/reads fasta file !
sub readSeqFromFasta{ my $file = $_[0]; my (%map,$id,$seq); open(IN,$file) or die("Cannot open file for reading $file:$!\n"); while(){ chomp; if($_ =~ /^>...2134 days ago
- ➜ trinityrnaseq-Trinity-v2.6.6 git:(master) ✗ ./Trinity --seqType fq --max_memory 250G --left /media/urbe/MyPassport/rnaseq_boris/AIG_AAAOSW_8_1_C1CBGACXX.IND11_noribo...
2128 days ago
- ➜ bin git:(master) ✗ ./fastq-dump --help Usage: ./fastq-dump [options] [...]...l-filter Filter used in early 1000 Genomes data: no...ter-1 Filter used in current 1000 Genomes...
2127 days ago
Long reads mapper bash script !
#!/bin/bash #only for LONG READS mapping #USAGE: runMapper.sh minimap2...echo "Name of the file used for mapping $fileName, present at $refFas...lName == "bwa" ]; then echo "Mapping with $toolName" $bwaMemLo...ame == "ngmlr" ]; then echo "Mapping with $toolName" if [ $reads...2123 days ago
- ➜ BorisTrinityAssembly /home/urbe/Tools/transrate-1.0.3-linux-x86_64/transrate...three kinds of metrics: 1. sequence based (if --assembly is given) 2. read mapping based (if --left and --right...
2124 days ago
- jitendra@jitendra-UNLOCK-INSTALL[SNP] wget https://github.com/broadinstitute/gatk/relea...awWgsMetrics (Picard) Collect whole genome sequencing-related metrics....ct metrics about coverage and performance of whole genome...
2076 days ago
Generates a genome coverage plot with R
library(CoverageView) ##draw a coverage plot for a test case BAM file #get a BAM test file treatBAMfile2056 days ago
Generate simulated polyploid genome !
#Generate 3% divergence msbar -point 4 -count 16558 toy.fasta > toyheterozygous3percent.fasta #Cat both files cat toy.fasta toymutated3percent.fasta > toyheteroz...2054 days ago
Installing pb-assembly on Linux !
[jnarayan@hmem00 ~]$ module avail -------------------------------------------------------- /usr/share/Modules/modulefiles ------------------------------------------...2035 days ago
- #http://www.nupack.org/downloads/source ➜ tools git:(master) ✗ cd nupack3.0.6 ➜ nupack3.0.6 git:(master) ✗ make make -C src/ make[1]: Entering directory '/home/ur...
2027 days ago
