Here is the canvas equivalent: https://bl.ocks.org/jodyphelan/5dc989637045a0f48418101423378fbd
Jody Phelan jodyphelan
jodyphelan
/ panoptes
Created
January 8, 2019 18:01
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| [0;32m Fetching dependancies[0m | |
| [0;32m Python dependancies[0m | |
| [0;32m NumPy...[0m | |
| Requirement already satisfied (use --upgrade to upgrade): numpy in ./panoptes_virtualenv/lib/python2.7/site-packages | |
| Cleaning up... | |
| [0;32m Panoptes requirements...[0m | |
| Downloading/unpacking https://github.com/cggh/DQXTableUtils/raw/master/dist/DQXTableUtils-0.1.1.tar.gz (from -r /home/jody/panoptes-master/server/REQUIREMENTS (line 1)) | |
| Downloading DQXTableUtils-0.1.1.tar.gz | |
| Running setup.py (path:/tmp/pip-8BJ9YK-build/setup.py) egg_info for package from https://github.com/cggh/DQXTableUtils/raw/master/dist/DQXTableUtils-0.1.1.tar.gz | |
jodyphelan
/ vbox
Last active
September 12, 2018 15:13
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| VBoxManage internalcommands sethduuid genomics_course_2018.vdi | |
| R | |
| VBoxManage modifyhd genomics_course_2018.vdi --resize 60000 | |
| wget http://pathogenseq.lshtm.ac.uk/ps_course/genomics_software.tgz | |
| tar -xvf genomics_software.tgz | |
| sudo bash aliview.install.run | |
| tar -xvf artemis.tar.gz | |
| sudo mv artemis /usr/local/src/ |
jodyphelan
/ programs
Last active
September 12, 2018 10:37
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| # Visualisation | |
| tablet | |
| #artemis | |
| #aliview | |
| # QC | |
| trimmomatic | |
| kraken | |
| fastqc |
jodyphelan
/ gist:d9b38fd79a11719a54eb5d7b097bdbaa
Last active
July 6, 2018 15:16
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| export THREADS=40 | |
| wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR187/008/ERR1873558/ERR1873558_1.fastq.gz | |
| wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR187/008/ERR1873558/ERR1873558_2.fastq.gz | |
| wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR210/001/SRR2101051/SRR2101051_1.fastq.gz | |
| wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR210/001/SRR2101051/SRR2101051_2.fastq.gz | |
| wget ftp://ftp.ensemblgenomes.org/pub/release-32/bacteria//fasta/bacteria_0_collection/mycobacterium_tuberculosis_h37rv/dna/Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.toplevel.fa.gz | |
| gunzip Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.toplevel.fa.gz | |
| mv Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.toplevel.fa H37Rv.fa |
jodyphelan
/ new test
Last active
May 4, 2018 08:27
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| export THREADS=40 | |
| time python filter_out_large_del_reads.py | |
| time seqtk subseq SRR6117388.sampled.fastq.gz test.filtered_read_names.txt | pigz -c > filtered_reads.fastq.gz | |
| ./minimap2/minimap2 -t $THREADS -R '@RG\tID:test\tSM:test\tPL:minION' -a -x map-ont H37Rv.fa filtered_reads.fastq.gz| ./samtools-1.8/samtools view -@ $THREADS -b - | ./samtools-1.8/samtools view -F 2048 - | ./samtools-1.8/samtools sort -@ $THREADS -o filtered.bam - | |
| samtools index -@ $THREADS filtered.bam | |
| splitchr.py H37Rv.fa 50000 --reformat | parallel --col-sep '\t' "./bcftools-1.8/bcftools mpileup -f H37Rv.fa filtered.bam -B -Q8 -a AD -r {1} | ./bcftools-1.8/bcftools call -mv -o filtered.{2}.bcf -Ob " |
jodyphelan
/ bcftools
Last active
May 2, 2018 23:45
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| git clone https://github.com/lh3/seqtk.git && cd seqtk && make && cd .. | |
| wget https://github.com/samtools/bcftools/releases/download/1.8/bcftools-1.8.tar.bz2 && tar -xvf bcftools-1.8.tar.bz2 && cd bcftools-1.8 && make && cd .. | |
| wget https://github.com/samtools/samtools/releases/download/1.8/samtools-1.8.tar.bz2 && tar -xvf samtools-1.8.tar.bz2 && cd samtools-1.8/ && make && cd .. | |
| git clone https://github.com/lh3/minimap2.git && cd minimap2 && make && cd .. | |
| wget https://zlib.net/pigz/pigz-2.4.tar.gz && tar -xvf pigz-2.4.tar.gz && cd pigz-2.4/ && make && cd .. | |
| wget ftp://ftp.ensemblgenomes.org/pub/release-32/bacteria//fasta/bacteria_0_collection/mycobacterium_tuberculosis_h37rv/dna/Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.toplevel.fa.gz | |
| gunzip Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.toplevel.fa.gz | |
| mv Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.toplevel.fa H37Rv.fa |
jodyphelan
/ stephane_plot
Last active
April 12, 2018 11:54
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| library(scales) | |
| library(data.table) | |
| setwd("~/projects/collaberations/stephane/") | |
| rawdata<-as.data.frame(fread("test.txt",header = T,stringsAsFactors = F)) | |
| head(rawdata) | |
| plot_vcf<-function(rawdata,start,end){ | |
| if (start==0 & end==0){ | |
| dat<-rawdata | |
| } else { |
jodyphelan
/ locus_plot
Created
January 11, 2018 19:06
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| library(data.table) | |
| small_indels<-read.table("~/gdr/assoc/pcaFiltered/indels/summary_stats/summary.indelReport.txt") | |
| bed<-read.table("genes.bed") | |
| big_dels<-read.table("big_indels.txt") | |
| if(!exists("snps")){snps<-as.data.frame(fread("snps.window.txt"))} | |
| plotLocus<-function(gene,window=5000){ | |
| gene_start <- bed[match(gene,bed$V4),2] | |
| gene_end <- bed[match(gene,bed$V4),3] | |
| lw <- gene_start-window |
jodyphelan
/ BCF merge error
Created
November 1, 2017 10:08
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| export THREADS=40 | |
| wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR103/003/ERR1035223/ERR1035223_1.fastq.gz | |
| wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR103/003/ERR1035223/ERR1035223_2.fastq.gz | |
| wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR166/009/ERR1664619/ERR1664619_1.fastq.gz | |
| wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR166/009/ERR1664619/ERR1664619_2.fastq.gz | |
| wget ftp://ftp.ensemblgenomes.org/pub/release-32/bacteria//fasta/bacteria_0_collection/mycobacterium_tuberculosis_h37rv/dna/Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.toplevel.fa.gz | |
| gunzip Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.toplevel.fa.gz | |
| mv Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.toplevel.fa H37Rv.fa |
jodyphelan
/ README.md
Last active
October 13, 2016 23:11
Force layout with SVG with zoom/pan and drag