Gene and transcript level quant using salmon

[jennaj]

Welcome @aperreault

Hopefully we can help!

I’m not sure where you are sourcing this but it is likely part of the problem with Salmon:

@aperreault

Using built-in hg38 transcriptome

Instead, try using a reference transcriptome fasta and a reference annotation GTF – both based on the same genome assembly version.

However, remember that you will probably not want to include the actual reference genome fasta! My guess is that including it was why you are getting this result:

@aperreault

nstead, they are divided by chromosome (first column is chr1, chr2, etc. and includes the non-standard chromosomes as well).

So – try using just the reads, along with the transcript fasta for the alignment portion and then the annotation to group those transcripts into genes. There will be two primary outputs. This is what is usually wanted to perform later downstream steps such as DESeq2.

UCSC is a good choice for human!

@jennaj

Try with these two files for human as an example of a paired set of reference data.

These are direct URLs – can be copied and pasted into the Upload tool. Leave all the auto settings at default.

• Fasta of transcripts https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/refMrna.fa.gz
• GTF representing those exact transcripts (plus associated genes) as mapped to the hg38 genomic assembly. https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/hg38.ncbiRefSeq.gtf.gz

Please give that a try and let us know if you would like any more help! See the banner topic for how/what to screenshot or to generate for history share link when getting more specific feedback.

Let’s start there!