tteximeta problem: couldn't find matching transcriptome, returning non-ranged SummarizedExperiment

Question

[tarek.mohamed]

Hi all,

I built the salmon index using the Gencode genome and transcriptomic sequence files. I then quantified my RNA fastq files and tried to use Teximeta (V1.20.3) to load the result to DESeq2. I encountered a problem related to the built-in taxomes. How can I fix it? I know that Teximeta supports Gencode format/files.

#code for building salmon index

 grep "^>" <(gunzip -c GRCh38.primary_assembly.genome.fa.gz) | cut -d " " -f 1 > decoys.txt

 sed -i.bak -e 's/>//g' decoys.txt

cat gencode.v48.transcripts.fa.gz GRCh38.primary_assembly.genome.fa.gz > grantome.fa.gz

#create index
salmon index --gencode -t /work/tmagdy/heps_nutr_rnaseq/PA/ref/salmon/gentrome.fa.gz -i /work/tmagdy/heps_nutr_rnaseq/PA/ref/salmon/salmon.indx --decoys /work/tmagdy/heps_nutr_rnaseq/PA/ref/salmon/decoys.txt -k 31

file1<-file.path("/Volumes/T7/ipsc_heps_rnaseq/salmon/quant/Control-1","quant.sf") 
file2<-file.path("/Volumes/T7/ipsc_heps_rnaseq/salmon/quant/Control-2","quant.sf") 
file3<-file.path("/Volumes/T7/ipsc_heps_rnaseq/salmon/quant/Control-3","quant.sf") 
file4<-file.path("/Volumes/T7/ipsc_heps_rnaseq/salmon/quant/PA-100-1","quant.sf") 
file5<-file.path("/Volumes/T7/ipsc_heps_rnaseq/salmon/quant/PA-100-2","quant.sf")
file6<-file.path("/Volumes/T7/ipsc_heps_rnaseq/salmon/quant/PA-100-3","quant.sf") 

files<- c(file1,file2,file3,file4,file5,file6)
file.exists(files)

coldata<-data.frame(files, names= c("cnt_1","cnt_2","cnt_3","pa_1","pa_2","pa_3"), condition=c(rep("control",3),rep("pa",3)),stringsAsFactors=FALSE)
coldata$files

se <- tximeta(coldata)
importing quantifications
reading in files with read_tsv
1 2 3 4 5 6 
couldn't find matching transcriptome, returning non-ranged SummarizedExperiment

> packageVersion("tximeta")
[1] '1.20.3'

[marco.barr]

Which code did you use to generate the salmon index?

Try to take a look at this link: https://github.com/thelovelab/tximeta/issues/38

[tarek.mohamed]

I updated the post with the code for index building

[marco.barr]

If you check carefullly your code, you created grantome.fa.gz but pointed Salmon at gentrome.fa.gz. Fix that first. Then, according to link, you can try to compute the checksum of your index, register and then load your txome. For example:

library(tximeta)

makeLinkedTxome(
  indexDir   = "/work/tmagdy/heps_nutr_rnaseq/PA/ref/salmon/salmon.indx",
  source     = "Gencode",
  organism   = "Homo sapiens",
  release    = "48",
  genome     = "GRCh38",
  fasta      = "/work/tmagdy/heps_nutr_rnaseq/PA/ref/salmon/gentrome.fa.gz",
  gtf        = "/work/tmagdy/heps_nutr_rnaseq/PA/ref/salmon/gencode.v48.annotation.gtf.gz",
  jsonFile   = "gencode.v48_GRCh38_gentrome.json"
)
  loadLinkedTxome("gencode.v48_GRCh38_gentrome.json") 

se <- tximeta(coldata)

Let me know,

Regards

Marco