GUI Quick Start

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'''PileLine GUI is under construction. We are currently working in PileLine GUI Quick Start.
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==PileLineGUI Input Files==
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[[File:Glez_Peña_et_al_Figure2.png|right|thumb|PileLine commands and accepted input files.]]
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'''PileLineGUI''' is capable to handle, filter and compare genomic position files (GP) including standard [http://samtools.sourceforge.net/pileup.shtml pileup], [http://genome.ucsc.edu/FAQ/FAQformat#format1 BED],[http://genome.ucsc.edu/FAQ/FAQformat#format3 GFF], or [http://1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcfv3.2 VCF] files.  
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The PileLine staff.
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Basically, GP are tabular files where the two first columns contain sequence name (i.e. chromosome name) and position coordinate respectively.
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Additional optional fields are accepted in '''PileLineGUI''', see an example of GP input file below:
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chr10    118829    optional1    optional2    optional3    ...   
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chr10    121207    optional1    optional2    optional3    ...
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chr10    121337    optional1    optional2    optional3    ...
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chr10    121636    optional1    optional2    optional3    ...
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==PileLineGUI Guided Example #1==
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==='''1.'''  '''Download''' and uncompress GP files (pileup format) and Annotation files to your working directory:===
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REFERENCE GENOME
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* Human Genome 18 in FASTA (.fa) and indexed FASTA (.fai). The sequence names are without the 'chr' prefix.
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:[http://sing.ei.uvigo.es/pileline/data/hg18.zip hg18.zip] (929MB)
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EXPERIMENT FILES
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* GP files-Experiment 1. Each .zip file contains 2 files: a complete and a variants-only pileup.
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:[[Media:Control1Files.zip|Control1Files.zip]] (36MB)
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:[[Media:Case1Files.zip|Case1Files.zip]] (36MB)
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'''Note: there is only data for the chromosome 10'''
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* GP files-Experiment 2. Each .zip file contains 2 files: a complete and a variants-only pileup.
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:[[Media:Control2Files.zip|Control2Files.zip]] (38MB)
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:[[Media:Case2Files.zip|Case2Files.zip]] (38MB)
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'''Note: there is only data for the chromosome 10'''
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ANNOTATION FILES
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* Gene Annotation .BED file.Ensembl Genes for the Human Genome 18.
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:[[Media:Hg18_hgnc_ensembl_genes.bed.zip|Hg18_hgnc_ensembl_genes.bed.zip]] (365KB)
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* SNPs from dbSNP version 36.3 for the Human Genome 18.
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:[[Media:DbSNP_36.3.bed.bgz.zip|DbSNP_36.3.bed.bgz.zip]] (150MB)
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==='''2. Compare 2 samples''' at variant level using '''''2smc.sh''''' functionality.===
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[[Media:2smc_help.pdf|Download]] the step-by-step tutorial to run 2smc functionality.
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==='''3. Compare N samples''' at position and gene level using '''''nsmc.sh''''' functionality.===
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[[Media:nsmc_help.pdf|Download]] the step-by-step tutorial to run nsmc functionality.
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==='''4. Annotate GP files.===
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[[Media:annotate_help.pdf|Download]] the step-by-step tutorial to annotate GP files with SNPs.
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[[Media:annotate2_help.pdf|Download]] the step-by-step tutorial to annotate GP files with Ensembl Genes.
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==='''5. Browse GP files.===
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[[Media:Browsing_help.pdf‎|Download]] the step-by-step tutorial to Browse GP files.

Latest revision as of 16:40, 22 February 2011

Contents

PileLineGUI Input Files

PileLine commands and accepted input files.

PileLineGUI is capable to handle, filter and compare genomic position files (GP) including standard pileup, BED,GFF, or VCF files.

Basically, GP are tabular files where the two first columns contain sequence name (i.e. chromosome name) and position coordinate respectively. Additional optional fields are accepted in PileLineGUI, see an example of GP input file below: 

chr10     118829     optional1     optional2     optional3     ...    
chr10     121207     optional1     optional2     optional3     ...
chr10     121337     optional1     optional2     optional3     ...
chr10     121636     optional1     optional2     optional3     ...


PileLineGUI Guided Example #1

1. Download and uncompress GP files (pileup format) and Annotation files to your working directory:

REFERENCE GENOME

  • Human Genome 18 in FASTA (.fa) and indexed FASTA (.fai). The sequence names are without the 'chr' prefix.
hg18.zip (929MB)


EXPERIMENT FILES

  • GP files-Experiment 1. Each .zip file contains 2 files: a complete and a variants-only pileup.
Control1Files.zip (36MB)
Case1Files.zip (36MB)

Note: there is only data for the chromosome 10

  • GP files-Experiment 2. Each .zip file contains 2 files: a complete and a variants-only pileup.
Control2Files.zip (38MB)
Case2Files.zip (38MB)

Note: there is only data for the chromosome 10


ANNOTATION FILES

  • Gene Annotation .BED file.Ensembl Genes for the Human Genome 18.
Hg18_hgnc_ensembl_genes.bed.zip (365KB)
  • SNPs from dbSNP version 36.3 for the Human Genome 18.
DbSNP_36.3.bed.bgz.zip (150MB)

2. Compare 2 samples at variant level using 2smc.sh functionality.

Download the step-by-step tutorial to run 2smc functionality.

3. Compare N samples at position and gene level using nsmc.sh functionality.

Download the step-by-step tutorial to run nsmc functionality.

4. Annotate GP files.

Download the step-by-step tutorial to annotate GP files with SNPs.

Download the step-by-step tutorial to annotate GP files with Ensembl Genes.

5. Browse GP files.

Download the step-by-step tutorial to Browse GP files.

Retrieved from "http://sing-group.org/pileline/index.php/GUI_Quick_Start"
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