Mouse GTF reference annotation

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1

Hello to the Galaxy community. Very helpful indeed. Many thanks for your effort.

I am new to sequencing and I am following the same Tutorial as above, but I am applying the protocol to mouse. Unfortunately, I ended up with the same problem, i.e., the final DEseq2 file did not contain the gene names, but instead the term N/A. I am using the file from UCSC web table, as follows:

Dataset Peek:

1.Seqname 2.Source 3.Feature 4.Start 5.End 6.Score 7.Strand 8.Frame 9.Attributes
chr1 mm10_ncbiRefSeq stop_codon 134202951 134202953 0.000000 - . gene_id “NM_001291928.1”; transcript_id “NM_001291928.1”;
chr1 mm10_ncbiRefSeq CDS 134202954 134203590 0.000000 - 1 gene_id “NM_001291928.1”; transcript_id “NM_001291928.1”;
chr1 mm10_ncbiRefSeq exon 134199215 134203590 0.000000 - . gene_id “NM_001291928.1”; transcript_id “NM_001291928.1”;
chr1 mm10_ncbiRefSeq CDS 134234663 134234733 0.000000 - 0 gene_id “NM_001291928.1”; transcript_id “NM_001291928.1”;

If I understood correctly I have not used the correct mouse file. Could you please help me, and point me to the correct file, and what I have done wrong, if not the wrong file?

Many thanks.

2

Hi @Brists,
could you share your Galaxy history with me? My email is Screenshot from 2022-04-03 16-52-09.

Regards

3

Hi gallardoalba,
Thanks for your email, appreciated. Following the instructions on the help site I realised the problem was the genome reference file from UCSC table platform. I downloaded the latest mouse genome from gencode and my problems about naming of genes and unassigned ambiguity were solved. However, there are other things that I would like to ask. Therefore, I open a new topic.

Many thanks again for your effort on the help tutorials.
Best regards,

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