txdb object for qCount ()

Question

[tarek.mohamed]

I am using QuasR to analyze mt paired end RNAseq data, now I have bam files for my 12 samples and the next step is to generate a count table for Differential gene expression analysis. I am using qCount() and for that I need to generate a txdb object. I have aligned my read to BSgenome.Hsapiens.NCBI.GRCh38.

• Can I get annotation file from BSgenome? So that I can use makeTxDbFromGFF to get TxDb
• Alternatively, I tried to generate a TxDb from biomart which was successful, but when calling qCount() I got an error (see below)

>TxDb<- makeTxDbFromBiomart(dataset="hsapiens_gene_ensembl")
>TxDb

TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: BioMart
# Organism: Homo sapiens
# Taxonomy ID: 9606
# Resource URL: www.ensembl.org:80
# BioMart database: ENSEMBL_MART_ENSEMBL
# BioMart database version: Ensembl Genes 83
# BioMart dataset: hsapiens_gene_ensembl
# BioMart dataset description: Homo sapiens genes (GRCh38.p5)
# BioMart dataset version: GRCh38.p5
# Full dataset: yes
# miRBase build ID: NA
# transcript_nrow: 217425
# exon_nrow: 735779
# cds_nrow: 295205
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2016-01-15 14:29:41 -0600 (Fri, 15 Jan 2016)
# GenomicFeatures version at creation time: 1.22.7
# RSQLite version at cr

>proj_RNASeq_geneLevels <- qCount(proj_RNASeq, TxDb, reportLevel="gene")

Error in qCount(proj_RNASeq, TxDb, reportLevel = "gene") : 
  sequence levels in 'query' not found in alignment files: CHR_HG126_PATCH, CHR_HG1342_HG2282_PATCH, CHR_HG1362_PATCH, CHR_HG142_HG150_NOVEL_TEST, CHR_HG151_NOVEL_TEST, CHR_HG1651_PATCH, CHR_HG1832_PATCH, CHR_HG2021_PATCH, CHR_HG2022_PATCH, CHR_HG2030_PATCH, CHR_HG2058_PATCH, CHR_HG2062_PATCH, CHR_HG2066_PATCH, CHR_HG2072_PATCH, CHR_HG2095_PATCH, CHR_HG2104_PATCH, CHR_HG2116_PATCH, CHR_HG2128_PATCH, CHR_HG2191_PATCH, CHR_HG2213_PATCH, CHR_HG2216_PATCH, CHR_HG2217_PATCH, CHR_HG2232_PATCH, CHR_HG2233_PATCH, CHR_HG2235_PATCH, CHR_HG2237_PATCH, CHR_HG2239_PATCH, CHR_HG2241_PATCH, CHR_HG2242_HG2243_PATCH, CHR_HG2244_HG2245_PATCH, CHR_HG2247_PATCH, CHR_HG2249_PATCH, CHR_HG2288_HG2289_PATCH, CHR_HG2290_PATCH, CHR_HG2291_PATCH, CHR_HG2334_PATCH, CHR_HG23_PATCH, CHR_HG26_PATCH, CHR_HG986_PATCH, CHR_HSCHR10_1_CTG1, CHR_HSCHR10_1_CTG2, CHR_HSCHR10_1_CTG3, CHR_HSCHR10_1_CTG4, CHR_HSCHR10_1_CTG6, CHR_HSCHR11_1_CTG1_1, CHR_HSCHR11_1_CTG1_2, CHR_HSCHR11_1_CTG2, CHR_HSCHR11_1_CTG3, CHR_HSCHR11

Tarek