robert-stuttaford

Query basics

{:db/ident       :meta/tag
 :db/valueType   :db.type/tuple
 :db/tupleAttrs  [:meta/tag-namespace :meta/tag-key :meta/tag-value] ;; all unique strings
 :db/cardinality :db.cardinality/one
 :db/unique      :db.unique/identity}

Then

andy-thomason

Genomics - A programmer's guide.

Andy Thomason is a Senior Programmer at Genomics PLC. He has been witing graphics systems, games and compilers since the '70s and specialises in code performance.

https://www.genomicsplc.com

lh3

This is a small experiment on the alignment of ~50bp INDELs. The query sequences are shown in 0.01.fq below, where seq_ori is a 204bp sequence extracted from the human reference genome, seq_del54 contains a 54bp deletion in the middle, seq_del84 contains a 84bp deletion in a 120bp read, and seq_ins40 contains a 40bp insertion in a 140bp read. These four short sequences were mapped to the human reference genome with Bowtie2, BWA-MEM, LAST, Novoalign, SNAP and Stampy with default settings. Non-default scoring functions were also tested for Bowtie2 (--rdg 5,1 --rfg 5,1), BWA-MEM (-A2 -E1) and LAST (-r2 -q4). The output by various mappers/settings can be found in this gist. The following table gives my summary:

Mapper	Setting	-84bp	-54bp	+40bp
BBMAP	default	Yes	Yes	Yes
Bowtie2	default	No	No	No
Bowtie2	--rdg 5,1 --rfg 5,1	as insertion	as insertion	Yes
BWA-MEM	default	as split	Yes	Yes
BWA-MEM	-A2 -E1	Yes	Yes	Yes
LAST	default	as split	as split

lh3

References:

• https://support.basespace.illumina.com/knowledgebase/articles/403618-python-run-downloader
• https://developer.basespace.illumina.com/docs/content/documentation/rest-api/api-reference

Steps:

1. Follow steps 1-5 in the first link above to acquire access_token. This will take a while, but you only need to do this once. Never share this token!!
2. Find the file you want to download. Copy the link, which looks something like: https://basespace.illumina.com/sample/9804795/files/tree/NA12878-L1_S1_L001_R1_001.fastq.gz?id=515013503. The "id" is the unique file identifier.
3. Download the file with: wget -O filename 'https://api.basespace.illumina.com/v1pre3/files/{id}/content?access_token={token}', where {token} is from step 1 and {id} from step 2.

arq5x

############################################################
# Novoalign
############################################################
export GENOME=/home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa.novo.k14.s1.idx
export IRCHOME=/net/midtier18/vol79/cphg-quinlan2/projects/irradiated-clones
export STEPNAME=ircnovo
export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=32000m:ncpus=16 -N $STEPNAME -m bea -M arq5x@virginia.edu";

echo "cd $IRCHOME; novoalign -d $GENOME -o SAM $'@RG\tID:parental\tSM:parental' -r Random \
             -f fastq/CgmW_AGTCAA_L001_R1.fastq.gz fastq/CgmW_AGTCAA_L001_R2.fastq.gz \

vsbuffalo

#!/bin/bash
# trim.sh - generic, slightly insane paired end quality trimming script
# Vince Buffalo <vsbuffaloAAAAAA@gmail.com> (sans poly-A)
set -e
set -u

## pre-config
ADAPTERS=illumina_adapters.fa
SAMPLE_NAME=some_sample_name
IN1=in1.fastq

brantfaircloth

Calling SNPs with GATK in non-model taxa

These notes build from several excellent sources:

• http://sfg.stanford.edu/
• http://www.broadinstitute.org/gatk/guide/
• http://www.broadinstitute.org/gatk/guide/topic?name=best-practices

and assume you're working with GATK 2.2-16. These notes also assume

jmchilton

import javax.net.ssl.HostnameVerifier;
import javax.net.ssl.SSLContext;
import javax.net.ssl.SSLSession;

import com.sun.jersey.api.client.config.ClientConfig;
import com.sun.jersey.api.client.config.DefaultClientConfig;
import com.sun.jersey.api.json.JSONConfiguration;
import com.sun.jersey.client.urlconnection.HTTPSProperties;

...

lynaghk

I 'm fleshing out some of these ideas here: https://github.com/lynaghk/todoFRP/tree/master/todo/angular-cljs

MohamedAlaa

tmux shortcuts & cheatsheet

start new:

tmux

start new with session name:

tmux new -s myname