Results for "BED files"
Bio-Scripts
library(vcfR) # Input the files. vcf2055 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 treatBAMfile2050 days ago
Generate simulated polyploid genome !
#Generate 3% divergence msbar -point 4 -count 16558 toy.fasta > toyheterozygous3percent.fasta #Cat both files cat toy.fasta toymutated3pe...2048 days ago
- ...tabix/ htslib-1.9/test/tabix/bed_file.Y.100200.out htslib-1.9/test/tabix/bed_file.bed htslib-1.9/test/tabix...-g -Wall -O2 -I. -c -o cram/files.o cram/files.c gcc -g -Wall...all -O2 -I. -fpic -c -o cram/files.pico cram/files.c gcc -g -Wa...
2014 days ago
Installing Platypus on Ubuntu !
...-g -Wall -O2 -I. -c -o cram/files.o cram/files.c gcc -g -Wal...all -O2 -I. -fpic -c -o cram/files.pico cram/files.c gcc -g -Wa...27/include/python2.7 -c tabix/bedidx.c.pysam.c -o build/temp.linux-x86_64-2.7/tabix/bedidx.c.pysam.o -Wno-incompatible-...2014 days ago
- $ sudo apt-get install rakudo [sudo] password for jit: Reading package lists......ng previously unselected package libjs-angularjs. (Reading database ... 185114 files and directories currently ins...
1546 days ago
Split the multifasta in separate files !
cat Avaga_allPalindrome.fa | awk '{ if (substr($0, 1, 1)==">") {filename=(substr($0,2) ".fa")} print $0 > filename }'1952 days ago
Samtools commands for bioinformatician !
## count mapped reads samtools view -c -F 260 mapping_...-b -S -o sal_sej.bam sal_sej.sam ### viewing bam files (view command) samtool view...ed file # ouput is file.bai # always index sorted files samtools index sal_sej_sorte...1598 days ago
- $ sudo apt install npm Reading package lists... Done Building dependency tree...00% Selecting previously unselected package gyp. (Reading database ... 180389 files and directories currently ins...
1548 days ago
Bash script to download SRA file !
#We can use the sratoolkit to directly pul...equencing run ID fastq-dump --split-files SRR1770413 #SRA stores dat...TQ for further processing. The --split-files part of the command ensures w...70413/SRR1770413.sra sra-dump --split-files SRR1770413.sra1554 days ago
