Hi all,

I have some raw RNA seq data from mouse that I would like to use DESeq2 for analysis. After using Salmon for quantification, I used tximport and DESeqDataSetFromTximport to create the data object, but the count matrix I obtained only have one row per sample, which is a value corresponding to protein-encoding.

I am not sure whether this is because the reference transcriptome I used for Salmon indexing is downloaded from http://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/cdna/, which should be GRCm38. However, the id names does not match those in the R package TxDb.Mmusculus.UCSC. The id names I obtained starts with "GENSCAN0000000000", and when I tried to convert it to tx2gene object, the result I obtained only has two columns, one is the id name and the other is the string 'protein encoding'. Below is the codes I used to create the tx2gene object.

gunzip -c Mus.GRCm38.cdna.all.fa.gz | grep '>' | cut -d ' ' -f1,4,7 > temp

paste <(cut -d '>' -f2 temp | cut -d ' ' -f1) <(cut -d ' ' -f2 temp | cut -d ':' -f2) <(cut -d ' ' -f3 temp | cut -d ':' -f2) >> tx2gene.txt

I am wondering whether there is any way to fix the issue or whether there is another fasta file I should use for Salmon index. Any help would be greatly appreciated!

It was common for users with tximport to have difficulty putting together the correct table for gene summarization, which is why we created tximeta which does this for you. Magic!

It works for GENCODE, Ensembl and RefSeq for human, mouse and fly. I'd recommend starting there first.