GUI Quick Start
From PileLine
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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. | 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 ''' | + | Additional optional fields are accepted in '''PileLineGUI''', see an example of GP input file below: |
chr10 118829 optional1 optional2 optional3 ... | chr10 118829 optional1 optional2 optional3 ... | ||
chr10 121207 optional1 optional2 optional3 ... | chr10 121207 optional1 optional2 optional3 ... | ||
chr10 121337 optional1 optional2 optional3 ... | chr10 121337 optional1 optional2 optional3 ... | ||
chr10 121636 optional1 optional2 optional3 ... | chr10 121636 optional1 optional2 optional3 ... | ||
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| + | |||
| + | |||
| + | ==PileLineGUI Guided Example #1== | ||
| + | |||
| + | ==='''1.''' '''Download''' and uncompress GP files (pileup format) and Annotation files to your working directory:=== | ||
| + | |||
| + | * Human Genome 18 in FASTA (.fa) and indexed FASTA (.fai). The sequence names are without the 'chr' prefix. | ||
| + | :[http://sing.ei.uvigo.es/pileline/data/hg18.zip hg18.zip] (929MB) | ||
| + | |||
| + | |||
| + | * GP files-Experiment 1. | ||
| + | Each .zip file contains 2 files: a complete and a variants-only pileup. | ||
| + | :[[Media:Control1Files.zip|Control1Files.zip]] (36MB) | ||
| + | :[[Media:Case1Files.zip|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. | ||
| + | :[[Media:Control2Files.zip|Control2Files.zip]] (38MB) | ||
| + | :[[Media:Case2Files.zip|Case2Files.zip]] (38MB) | ||
| + | '''Note: there is only data for the chromosome 10''' | ||
| + | |||
| + | |||
| + | * Gene Annotation .BED file.Ensembl Genes for the Human Genome 18. | ||
| + | :[[Media:Hg18_hgnc_ensembl_genes.bed.zip|Hg18_hgnc_ensembl_genes.bed.zip]] (365KB) | ||
| + | |||
| + | * SNPs from dbSNP version 36.3 for the Human Genome 18. | ||
| + | :[[Media:DbSNP_36.3.bed.bgz.zip|DbSNP_36.3.bed.bgz.zip]] (150MB) | ||
Revision as of 12:43, 21 February 2011
PileLineGUI 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:
- Human Genome 18 in FASTA (.fa) and indexed FASTA (.fai). The sequence names are without the 'chr' prefix.
- hg18.zip (929MB)
- 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
- 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)
