makeTxDbFromGFF Error due to incompatible seqnames
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Entering edit mode
filipeje • 0
@filipeje-13493
Last seen 4.2 years ago

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            

 
 
 
summarizedexperiment TxDb gtf genomicfeatures • 800 views
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Entering edit mode

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.

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Entering edit mode

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.

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