Data Requirements
From GersteinInfo
User documentation main
Here is the list of required data for a comprehensive use of FusionSeq tools.
External
- Homo Sapiens Reference genome (hg18): the user should download both chromFa.zip and hg18.2bit.
The human genome needs to be properly indexed to be used by bowtie. Please see the instruction of bowtie for performing this operation. Indicatevely, you would need to run something like:
$ bowtie-build -f hg18_nh.fa /path2bowtieIndex/hg18_nh/
where hg18_nh.fa corresponds to the concatenation of all human chromosomes from chromFa.zip without the different haplotypes and "random" stuff.
Provided
The following data sets, bundled in a tarball, can be downloaded here.
- knownGeneAnnotation.txt
- knownGeneAnnotationTranscriptCompositeModel.txt
- knownGeneAnnotationTranscriptCompositeModel.fa
- kgXref.txt
- knownToTreefam.txt
The composite model needs to be indexed by bowtie:
$ bowtie-build -f knownGeneAnnotationTranscriptCompositeModel.fa /path2bowtieIndex/hg18_knownGeneAnnotationTranscriptCompositeModel/hg18_knownGeneAnnotationTranscriptCompositeModel
Please make sure that the correct filenames are used.
