Today's bioinformatics lesson is brought to you by the letter 'W'

by

Keith Bradnam

Image from flickr.com/91619273@N00/

Today's bloinformaties lessonis brought to you by the letter 1W1

Image from flickr.com/91619273©NO0/

Wis for Workflowsis for Workflows

A typical bioinformatics workflow

Illumina data(FASTQ format)

Remove adapter contamination

A typical bioinformatics workflow

Remove adapter contamination

A typical bioinformatics workflow

Illumina data(FASTQ format)

Remove adapter contamination

scythe cutadapt trimgalore

skewer Btrim

Trimmomatic

A typical bioinformatics workflow

Remove adapter contamination

scythecutadapttrimgaloreskewerBtrim

Trimmomatic

A typical bioinformatics workflow

Illumina data(FASTQ format)

Remove adapter contamination

scythe cutadapt trimgalore

skewer Btrim

Trimmomatic

Lots of tools you could use!

A typical bioinformatics workflow

Lots of toolsyou could use!

Remove adapter contamination

scythecutadapttrimgaloreskewerBtrim

Trimmomatic

Trim reads for low quality bases

sickle Qtrim

FastQC FastX

PRINSEQ Trimmomatic

Trim reads for low quality bases

sickleQtrim

FastQCFastX

PRINSEC)Trimmomatic

Map reads to genome/transcriptome

BWA Bowtie TopHat SHRiMP BFAST MAQ

From ebi.ac.uk/~nf/hts_mappers/

There are a lot of read mappers out there!

From ebi.ac.uk/-nf/hts_mappers/ H I S A T •-JAGuaR • -BWA-PSSM • - -MOSAIK •- - - - - -Hobbes2 •CUSHAW3 a-

NextGenMap •Subread/Subjunc •CRAC •-SRmapper •-GEM •STAR •ERNE •-BatMelh •-BLASR a-YAHA •

SeciAlto •Batmis •There are a lot ofDynMaPp O S A •

ContextMap •-as?n1 •-RUM a_read mappers out there! StampydrFAST •-Bismark •-•-

MapSplice a- REAL a--BS-Seeker a-- - B S - S e e k e r 2 - ••SupersplatliceMapRAT • - B R A T - S W -•-BFAST •-

segemeht •-GNUMAP •-GenomeMapper •-mrFAST • • - mrsFAST m r s FA S T- L i l t r a - -• - - - -PerM • - - - - - - --RNA-Mate • - - - X-Mate a- - - - SBSMAP • - - - - S p l a z e rRazerS • --•- -MicroRazerS - • - - • RazerS3SHRIMP a — —• SHR1MP2 -•BWA s - - • BWA-SWCloudBurst •ProbeMatch • • W H A M - •

TopHat a- T o p H a t 2 -•-Bowlie •- B o w t i e 2 •-MOM 4-PASS •- P A S S - b i s - -•Slider • - - -Slider-II-()PALMA •SOCS "-MAO •SegMap •ZOOM •PalMaN a-RMAP •SOAP • —SOAP2- -•BWT-SW • - - S O A P S p l i c e - -•

Blat a-SSAHA •

GMAP •Exonerate •Mummer 3 •

ELAND • GSNAP- a-

2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015Years

Map reads to genome/transcriptome

BWA Bowtie TopHat SHRiMP BFAST MAQ

From ebi.ac.uk/~nf/hts_mappers/From eloi.ac.uki-ntiGnotdrni et Atft.- 2 c 1 4 . 1.5auppl 9:512hitk.,:,www.bicrileckentrakuoiryt41-2105/75.•9•512

HISATJAGuaIR - -Bw •A-PSSM - - - -M0-A1K

ApproachARYANA: Aligning Reads by Vet Another

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Availability: ARYAN.4 compip7e source rexie can he obrairteil from kittp.//gitbubcOrnlar)'ana-aligner

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Filter for uniquely mapped reads

SAMtools Picard GATK Unix

Filter for uniquely mapped reads

SAMtoolsPicardGATKUnix

Filter for high quality alignments

SAMtools Picard GATK Unix

Filter for high quality alignments

SAMtoolsPicardGATKUnix

Data suitable for final analysis

Data suitable forfinal analysis

Some questions you should ask yourself…Some questions you should ask yourself..

Wis for 'Why?'is for 'Why?

Why are each of these steps needed?Why are each of these steps needed?

Why should I use tool 'X' at this step?Why should I use tool X' at this step?

Wis for 'What?'is for 'What?'

What is the effect on running each step?What is the effect on running each step?

What is a good result?What is a good result?

The effect of applying many 'bioinformatics axes'

Illumina data(FASTQ format)

2 FASTQ files

Files are ~6.5 GB

52.5 million reads total

The effect of applying many1bloinformatics axes'

IIlumina data(FASTQ format)

2 FASIQ files52.5 million reads total

Files are ,-,64.5 GB

Remove adapters & trim

50.1 million reads

Remove adapters & trim

50.1 million reads

Align to transcriptome with Bowtie

35.8 million reads map

Align to transcriptome with Bowtie

35.8 million reads map

Filter for uniquely mapped reads

31.4 million reads align uniquely

Filter for uniquely mapped reads

31.4 million reads align uniquely

Filter for high quality alignments

22.7 million reads have alignment scores of zero

Filter for high quality alignments

22.7 million reads have alignment scores of zero

Data suitable for final analysis

Reduced data from 52.5 to 22.7 million reads

Data suitable forfinal analysis

Reduced data from 52.5 to 22.7 million reads

It can be helpful to know how the different steps in a workflow reduce your data

It can be helpful to know how the differentsteps in a workflow reduce your data

One final tip…One final tip...

ls -ltris l t r

Run this command after every step of a workflowRun this command afterevery step of a workflow

Let's you see whether output files were actually created

Let's you see whether output fileswere actually created

Let's you see whether output files contain any data

Let's you see whether output filescontain any data

Most recently modified files will be at bottom of your terminal windowMost recently modified files will beat bottom of your terminal window

The endThe end