Question: Tximport Error ... unable to match up my quant.sf and tx2gene columns
0
gravatar for 2405592M
4 months ago by
2405592M90
2405592M90 wrote:

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)
rna-seq salmon tximport • 168 views
ADD COMMENTlink written 4 months ago by 2405592M90

Did you index with the gencode flag?

ADD REPLYlink written 4 months ago by ATpoint40k

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

ADD REPLYlink written 4 months ago by 2405592M90
1
gravatar for ATpoint
4 months ago by
ATpoint40k
Germany
ATpoint40k wrote:

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?

ADD COMMENTlink written 4 months ago by ATpoint40k
2

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!

ADD REPLYlink written 4 months ago by 2405592M90
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 850 users visited in the last hour