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Question: makeTxDbFromGFF Error due to incompatible seqnames
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gravatar for filipeje
4 months ago by
filipeje0
filipeje0 wrote:

Hi,

I am trying to create TxDb files and i am using the bioconductor guide (here: https://www.bioconductor.org/help/workflows/rnaseqGene/) as a reference.

However i am having issues with the sequence naming in the gtf file. 

library(Rsubread)
library("Rsamtools")
library("GenomicFeatures")

cell <- factor(c("CAT.S", "CAT.S", "IL13NG", "IL13NG", "LOX.1", "LOX.1")) file <- c("A_ACAGTG/sorted.bam", "B_GCCAAT/sorted.bam", "C_CAGATC/sorted.bam", "D_CTTGTA/sorted.bam", "E_AGTCAA/sorted.bam", "F_GTGAAA/sorted.bam")
data <- data.frame(cell, file)
bamfiles <- BamFileList(file) seqinfo(bamfiles[1])
gtffile <- "CriGri_1.0.gtf"
txdb <- makeTxDbFromGFF(gtffile, format = "gtf", dbxrefTag = "GeneID") head(gtffile)

This is the output I am receiving:

> txdb <- makeTxDbFromGFF(gtffile, format = "gtf", dbxrefTag = "GeneID")
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... Error in .merge_transcript_parts(transcripts) : 
  The following transcripts have multiple parts that cannot be merged because of incompatible seqnames: NM_001243977.1,
  NM_001244004.1, NM_001244022.1, NM_001244033.1, NM_001244041.1, NM_001244052.1, NM_001244378.1, NM_001246707.1, NM_001246723.1,
  NM_001246741.1, NM_001246788.1, NM_001246827.1, NM_001246828.1, NR_045132.1

this is my session info

sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.9 (Santiago)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] GenomicFeatures_1.26.4 AnnotationDbi_1.36.2   Biobase_2.34.0         BiocInstaller_1.24.0   Rsamtools_1.26.2       Biostrings_2.42.1     
 [7] XVector_0.14.1         GenomicRanges_1.26.4   GenomeInfoDb_1.10.3    IRanges_2.8.2          S4Vectors_0.12.2       BiocGenerics_0.20.0   
[13] bindrcpp_0.2           Rsubread_1.24.2        dplyr_0.7.1            tidyr_0.6.3            edgeR_3.16.5           limma_3.30.13         

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.11               bindr_0.1                  bitops_1.0-6               tools_3.3.2                zlibbioc_1.20.0           
 [6] biomaRt_2.30.0             digest_0.6.9               bit_1.1-12                 RSQLite_2.0                memoise_1.0.0             
[11] tibble_1.3.3               lattice_0.20-34            pkgconfig_2.0.1            rlang_0.1.1                Matrix_1.2-7.1            
[16] DBI_0.7                    rtracklayer_1.34.2         locfit_1.5-9.1             bit64_0.9-7                grid_3.3.2                
[21] glue_1.1.1                 R6_2.1.2                   XML_3.98-1.9               BiocParallel_1.8.2         blob_1.1.0                
[26] magrittr_1.5               GenomicAlignments_1.10.1   SummarizedExperiment_1.4.0 assertthat_0.2.0           RCurl_1.95-4.8            

 
 
 
ADD COMMENTlink modified 4 months ago by Michael Love15k • written 4 months ago by filipeje0

makeTxDbFromGFF is a function in the GenomicFeatures package, so I added this to the tags of the post. It's a good idea to tag the relevant package so you can get advice from the package maintainers.

ADD REPLYlink modified 4 months ago • written 4 months ago by Michael Love15k

Hi,

Something looks wrong with your GTF file. Do you think you can make it available somewhere so we can look at it? Thanks,

H.

ADD REPLYlink modified 4 months ago • written 4 months ago by Hervé Pagès ♦♦ 13k
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