Demo of Galaxy

http://main.g2.bx.psu.edu/

http://galaxy.tuebingen.mpg.de/

1. Upload data or download data from database

Upload Oct4 binding regions from local computer to galaxy

Get data -> Upload you file from your computer -> Choose BED file format -> Locate the file on your computer -> Choose genome mm8 -> Execute

Get promoter regions of all mouse genes from UCSC genome server

Get data -> UCSC Main table browser -> get output -> Choose Upstream by 1000 bases -> Send query to Galaxy

Get coding regions of all mouse genes from Biomart server

Get data -> Choose ENSEMBL 56 GENES -> Choose Mus musculus genes -> Attributes: GENE -> Choose Ensembl Gene ID, Chromosome Name, Gene Start, Gene End, Strand -> Results -> Go

2. Change the coordinates between assemblies of genomes

Lift-over -> Convert genome coordinates between assemblies and genomes -> Convert coordinates of Oct4_Binding.bed -> To: mm9 -> Execute

3. Text Manipulation

Add column to an existing query -> add this value: 1 -> to Query: Oct4_binding.bed -> Iterate: YES -> Execute

Cut column from a table -> Cut columns: c1,c2,c3,c4,c5,c6 -> Delimited by: Tab -> From: table name -> Execute

4. Convert Formats

BED-to-GFF converter -> Convert this query: Oct4_Binding.bed -> Execute

Upload fastqdemo file -> FASTQ to FASTA converter -> FASTQ Library to convert: fastq_demo.fastq -> Discard sequences with N bases: yes -> Rename: yes -> Execute

5. FASTA manipulation

Compute sequence length -> select the fasta file -> Execute

6. Filter and Sort

Filter -> Filter: Oct4_Binding.bed -> with following condition: c1==’chr3’ -> Execute

7. Extract features

Get gene data from UCSC server -> Gene BED To Exon/Intron/Codon BED expander -> Coding Exons + UTR Exons -> from: gene data -> Execute

8. Fetch sequences

Extract Genomic DNA using coordinates from assembled/unassembled genomes -> Output data type: FASTA -> Execute

9. Fetch Alignments

Extract Pairwise MAF blocks given a set of genomic -> Bed file -> MAF source: hg18, mm9 -> Execute

10. Operate on Genomic Intervals

Intersect the intervals of two queries -> Overlapping Intervals -> of: Promoter bed file -> that intersect: Oct4_Binding.bed -> for at least 1 bp -> Execute

11. Next Generation Sequencing ToolBox

Preprocessing:

NGS: QC and manipulation -> FASTQ Groomer converts any FASTQ to Sanger -> Fastqdemo.fastq -> Illumina 1.3+ -> Execute

Compute quality statistics -> Fastq Groomer data -> Execute

Draw quality score boxplot -> Fastq Groomer data -> Execute

Draw nucleotides distribution chart -> Fastq Groomer data -> Execute