Asboner: Created page with '{{FusionSeqHeader}} Here is the list of required data for a comprehensive use of FusionSeq tools. ===External=== *[http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/ Homo …'

2010-08-19T13:05:01Z

Created page with '{{FusionSeqHeader}} Here is the list of required data for a comprehensive use of FusionSeq tools. ===External=== *[http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/ Homo …'

New page

{{FusionSeqHeader}}
Here is the list of required data for a comprehensive use of FusionSeq tools.

===External===
*[http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/ 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 [http://rnaseq.gersteinlab.org/tarballs/FusionSeq_Annotation_Data_1.0.tar.gz 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.

Data Requirements - Revision history

Asboner: Created page with '{{FusionSeqHeader}} Here is the list of required data for a comprehensive use of FusionSeq tools. ===External=== *[http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/ Homo …'