I have used Salmon tool to quantify and was doing further analysis in R for Ref-based RNAseq. While using
txi.salmon function I came across this error :
reading in files with read_tsv 1 2 3 4 Error in .local(object, ...) : 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 IDs (file): [NMUH01000001.1, NMUH01000002.1, NMUH01000003.1, ...]
Example IDs (tx2gene): [rna-gnl|WGS:NMUH|Taro_000008-RA_mrna, rna-gnl|WGS:NMUH|Taro_000009-RA_mrna, rna-gnl|WGS:NMUH|Taro_000015-RA_mrna, ...]
I understand that the IDs in the txdb object and the quant.sf files are different. This is the gff file I have used :
My quant.sf file:
The IDs in quant.sf are sequence names and not the corresponding transcript IDs. This is really confusing me. If this has something to do with quantifying what should be changed ? Hope anyone would help me with this.
Thanks in advance.