Get 10% of triobra1 and calculate REAP /projects/relatedness/plink-1.07-x86_64/plink –file trio1_bra.phasing –thin 0.2 –noweb –geno 0 –recode –out trio1_bra.phasing.20 /projects/relatedness/plink-1.07-x86_64/plink –file trio1_bra.phasing –thin 0.1 –noweb –geno 0 –recode –out trio1_bra.phasing.10 Of these, 956761 snps are new, 5637 already exist Cálculo só com os brasileiros merge3.ped
Relatório de Atividades LGC
Report 210213
Vcf::throw(‘Vcf4_1=HASH(0x1ce37c8)’, ‘The command “tabix -l /projects/1000genomes/integrated_call_s…’) called at /lgc/programs/vcftools_0.1.10/lib/perl5/site_perl/Vcf.pm line 2630
VcfReader::get_chromosomes(‘Vcf4_1=HASH(0x1ce37c8)’) called at /lgc/programs/vcftools_0.1.10/bin/vcf-merge line 195
main::init_cols(‘HASH(0x18d5c18)’, ‘Vcf4_1=HASH(0x18dcd30)’) called at /lgc/programs/vcftools_0.1.10/bin/vcf-merge line 277
main::merge_vcf_files(‘HASH(0x18d5c18)’) called at /lgc/programs/vcftools_0.1.10/bin/vcf-merge line 12
Traceback (most recent call last):
File “/lgc/scripts/reap.py”, line 51, in
Report 20/11/12
1000genomes data
unlimited storage
http://www.thewebhostingdir.com/shared-hosting/unlimited-data-transfer-hosting/
Where I can store 1000 files of 1.2GB or or 1 file of 7TB ?
Report 10/10/12
http://watson.nci.nih.gov/bioc_mirror/packages/release/bioc/vignettes/GenomicFeatures/inst/doc/GenomicFeatures.pdf
http://www.bioconductor.org/packages/2.11/bioc/manuals/GenomicFeatures/man/GenomicFeatures.pdf
http://bioconductor.org/help/course-materials/2010/SeattleIntro/GenomicFeatures.pdf
Page 6 exactly what we need.
http://www.bioconductor.org/help/course-materials/2012/BioC2012/ranges.R
http://bioconductor.org/packages/release/bioc/vignettes/GenomicFeatures/inst/doc/GenomicFeatures.pdf
Report 02/10/12
Bioconductor Libraries to learn
http://www.bioconductor.org/packages/2.10/bioc/vignettes/topGO/inst/doc/topGO.pdf
Keggapi
Updated R to version 2.15
echo "deb http://cran.mirrors.hoobly.com/bin/linux/ubuntu precise/" >> /etc/apt/sources.list gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9 gpg -a --export E084DAB9 | sudo apt-key add -
Installed
http://www.omegahat.org/RCurl/FAQ.html
Biomart
library(KEGGSOAP)
genes <- get.genes.by.pathway(“path:hsa04340”)
#for each gene
genes <- sub(“(hsa:)”, “”, genes)
length(genes)
genes
#biomart
library(“biomaRt”)
ensembl = useMart(“ensembl”,dataset=”hsapiens_gene_ensembl”)
goids = getBM(attributes=c(‘entrezgene’,’go_id’), filters=’entrezgene’, values=genes, mart=ensembl)
Report 21/09/12
Indel Detection
Atlas, Dindel
ruby1.9.1 /lgc/programs/Atlas2_v1.4.1/Atlas-Indel2/Atlas-Indel2.rb -b ../../input/Exome_1_RP.realigned-recalibrated.bam -r /lgc/datasets/gatk_data/hg19/ucsc.hg19.fasta -o rms_indel -S
Varid Indel
varid_exec -a ../../../../input/Exome_1_RP.realigned-recalibrated.sam -r /lgc/datasets/gatk_data/hg19/ucsc.hg19.fasta -o varid_rms_detection –threads 4 –format vcf
Phasing Beagle
Replication studies: Bad copy
This week I read an article about how hard is to replicate published studies.
http://www.nature.com/news/replication-studies-bad-copy-1.10634
Libraries to generate plot for Bioinformatics
Less without WordWrap
To visualize big files on terminal without linebreaks you can use the command “less -S”
Cursos
Curso de R
http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-Running-SOAP
Curso de Python
http://code.google.com/edu/languages/google-python-class/