gene ids do not have corresponding valid gene names kallisto bus tools

Question

[naili mortadha]

hello everyone i retrieved raw unmapped data from GEO and mapped them using python wrapper kb for kallisto bustools and it shows this message :

WARNING [count] 22588 gene IDs do not have corresponding valid gene names. These genes will use their gene IDs instead.(how to deal with this, i read their paper and they didn’t address dealing with nameless gene ids)

this number varies whether i used the default reference and index or i created my own.

these are the commands i used : mapping and generating the matrix command :

time kb count --h5ad -i index.idx -g t2g.txt -x 10xv3 -o output --filter bustools -t 8 -m 7G  SRR28245473_1.fastq  SRR28245473_2.fastq

using default index :

 kb ref -d human -i index.idx -g t2g.txt -f1 transcriptome.fasta

creating ur index :

kb ref -i transcriptome.idx -g transcripts_to_genes.txt -f1 cdna.fa Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa Homo_sapiens.GRCh38.112.gtf

Answer 1

[dsull]

This isn't really a kb-python issue; it's a GTF annotation issue. Nameless gene IDs is not something that can be fixed -- if the GTF file doesn't have a gene name associated with it, there's really nothing that can be done.

For example, the gene ENSG00000228037 literally has no gene name; the only thing that can be done is putting "ENSG00000228037" as its gene name.

The reason the default index has a different number of genes is because the default index doesn't include stuff like pseudogenes (basically, it tries to follow Cell Ranger's list of genes as closely as possible).

I don't see any problem here.

[naili mortadha]

thank you so much but how to deal with them in downstream analysis ?

[dsull]

Just use them as if they are any other gene (they are the same as every other gene, we just don't have official names for them).