refGenes_hg19: Gene annotation files for hg19, mm9 and mm10.

In calabrialab/ISAnalytics: Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

Gene annotation files for hg19, mm9 and mm10.

Description

This file was obtained following this steps:

1. Download from http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ the refGene.sql, knownGene.sql, knownToRefSeq.sql, kgXref.sql tables

2. Import everything it in mysql

3. Generate views for annotation:

SELECT kg.`chrom`, min(kg.cdsStart) as CDS_minStart,
max(kg.`cdsEnd`) as CDS_maxEnd, k2a.geneSymbol,
kg.`strand` as GeneStrand, min(kg.txStart) as TSS_minStart,
max(kg.txEnd) as TSS_maxStart,
kg.proteinID as ProteinID, k2a.protAcc as ProteinAcc, k2a.spDisplayID
FROM `knownGene` AS kg JOIN kgXref AS k2a
ON BINARY kg.name = k2a.kgID COLLATE latin1_bin
-- latin1_swedish_ci
-- WHERE k2a.spDisplayID IS NOT NULL and (k2a.`geneSymbol` LIKE 'Tcra%' or
k2a.`geneSymbol` LIKE 'TCRA%')
WHERE (k2a.spDisplayID IS NOT NULL or k2a.spDisplayID NOT LIKE '')
and k2a.`geneSymbol` LIKE 'Tcra%'
group by kg.`chrom`, k2a.geneSymbol
ORDER BY kg.chrom ASC , kg.txStart ASC

Usage

data("refGenes_hg19")

data("refGenes_mm9")

Format

An object of class tbl_df (inherits from tbl, data.frame) with 27275 rows and 12 columns.

An object of class tbl_df (inherits from tbl, data.frame) with 24487 rows and 12 columns.

Functions

• refGenes_mm9: Data frame for murine mm9 genome

calabrialab/ISAnalytics documentation built on Nov. 2, 2023, 8:57 p.m.