Help on GeneID output

usegalaxy.org support
, ,
1

Hello, I followed this workflow 1: RNA-Seq reads to counts. I was able to generate my feature count data for each of my samples using the parameters in the workflow.

Here is an example of the output:

|Geneid |barcode92.fastq|
|IZ85_01250| 7|

I am having a hard time getting the geneid matched to a database. Can you offer any insight into which database? I used ncbi reference from salmonella gtf file and the annotated genes.

I found some hits when I enter in UNIPARC? However, I do not get one gene for each entry, there are multiple.

Thanks for any support given on this.

Genesis

2

Hi @gherrera
the tutorial you’ve mentioned uses mouse data, and the second tutorial uses AnnotateMyID. This tool is available for small number of species.
To extract additional information, such as full gene name etc, from the gtf file maybe try Extract features from GFF data and/or text manipulation tools. The exact steps depend on the annotation file you have.
Hope that helps.
Kind regards,
Igor