Tximport Error ... unable to match up my quant.sf and tx2gene columns

Question

[2405592M]

I got the following error when using Tximport to load my salmon quant.sf files:

None of the transcripts in the quantification files are present in the first column of tx2gene. Check to see that you are using the same annotation for both.

example ID [ENST00000568077.5|ENSG00000130731.16|OTTHUMG00000047855.5|OTTHUMT00000421794.1|METTL26-211|METTL26|588|UTR5:1-41|CDS:42-353|UTR3:354-588|

I know the issue is because i need to have a space between the transcript ID and the |

If I'm using file.path to import all my quant.sf files into R, is there a way of correcting this space issue for all files?

dir <- "/mnt/data/BM/Total_RNAseq/salmon/protein_coding"

files <- file.path(dir, samplefile$sampleID, "quant.sf")

annotation_transcript <- elementMetadata(import(gtf_file, feature.type = "transcript"))

tx2gene <- annotation_transcript[,c("transcript_id", "gene_id")]

txi.salmon <- tximport(files, type = "salmon", tx2gene = tx2gene)

[ATpoint]

Did you index with the gencode flag?

[2405592M]

Sorry I don't follow. What do you mean by gencode flag?

Answer 1

[ATpoint]

You apparently used salmon to quantify your reads. This requires an index. You can pass the --gencode flag during indexing so that the transcript name is capped after the first | avoiding the situation you encounter.

Anyway, can you post an example of your tx2gene map and some lines of one of the quant.sf files?

[2405592M]

I fixed the error using the tag you suggested

salmon index -t gencode.vM25.pc_transcripts_filtered.fa -i gencode.vM25.pc_transcripts_f_index --gencode -p 30

Worked beautifully! Thank you!