Pawel Szczesny freesci
freesci
/ gist:5240374
Created
March 25, 2013 20:24
Creating an annotation database in Bioconductor for non-model organism
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| source("http://bioconductor.org/biocLite.R") | |
| library(AnnotationForge) | |
| makeOrgPackageFromNCBI(version="0.0.1",author="PS",maintainer="PS <ps@pawelszczesny.org>",outputDir=".",tax_id=4081,genus="Solanum", species="lycopersicum") | |
| #here you need to wait a bit, few hours maybe | |
| install.packages("org.Slycopersicum.eg.db", repos=NULL, type="source") | |
| library("org.Slycopersicum.eg.db/") | |
| keys<-head(keys(org.Slycopersicum.eg.db)) | |
| head(select(org.Slycopersicum.eg.db, keys=keys,cols=c("ENTREZID","ACCNUM","ALIAS","CHR","PMID","REFSEQ","SYMBOL","UNIGENE" ,"GENENAME")) |
freesci
/ consensus_from_mapping
Created
March 25, 2013 14:48
Create consensus sequences from mapping reads onto multifasta reference. For background see: http://www.biostars.org/p/65903/
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| bwa index database.fasta | |
| bwa aln -t #num_threads database.fasta reads.fastq > reads.sai | |
| bwa samse database.fasta reads.sai reads.fastq > aln.sam | |
| samtools view -b -o aln.bam aln.sam | |
| samtools sort aln.bam aln.sorted | |
| samtools index aln.sorted.bam | |
| samtools mpileup -uf database.fasta aln.sorted.bam |bcftools view -cg - |vcfutils.pl vcf2fq >aln.fastq |