Hello everyone,
I have a count matrix that was created using Salmon. I used version 6 of the chicken transcriptome (https://ftp.ensembl.org/pub/release-106/fasta/gallus_gallus/cdna/Gallus_gallus.GRCg6a.cdna.all.fa.gz) and genome (https://ftp.ensembl.org/pub/release-106/fasta/gallus_gallus/dna/Gallus_gallus.GRCg6a.dna.toplevel.fa.gz) from Ensembl to create the index and decoy files.
When I imported the results into R, I used Ensembl 106 EnsDb for Gallus gallus to convert transcript level to gene level counts using the following R code:
ensdb_query ← query(hub, c(“EnsDb”, “gallus gallus”, “106”))
ensdb_query
ensdb_106 ← ensdb_query[[‘AH100636’]]
tx_data ← transcripts(ensdb_106, return.type = “DataFrame”)
tx2gene ← tx_data[, c(“tx_id”, “gene_id”)]
txi ← tximport(quant_files, type = “salmon”, tx2gene = tx2gene,ignoreTxVersion = TRUE)
I then exported the count matrix of all samples into a tab-delimited file with the meta-data.
When I try to import it into ExpressAnalyst, I get the same error message as in this post (ExpressAnalyst not recognizing ID type) indicating 0% match of gene ids. From the previous post on this issue, it is not very clear if this issue was resolved.
Here is a short list of genes from my data:
ENSGALG00000000003
ENSGALG00000000011
ENSGALG00000000038
ENSGALG00000000044
ENSGALG00000000048
ENSGALG00000000055
ENSGALG00000000059
ENSGALG00000000067
ENSGALG00000000071
ENSGALG00000000081
ENSGALG00000000086
ENSGALG00000000091
ENSGALG00000000094
ENSGALG00000000102
ENSGALG00000000104
ENSGALG00000000106
Any advice?
Many thanks.