Question: Htseq-count: How to add id attribute and additional attributes in Galaxy (RNA-seq)
gravatar for adhikari_satish
7 months ago by
adhikari_satish0 wrote:

Hello, I am working with a bacterial genome. I'm using DESeq2 for differential gene expression analysis between WT and mutant. Before using DESeq2, I need to make a count table. So, I use Htseq-count. Below is my a portion of my gff file:

NC_014375.1 RefSeq gene 273 1709 . + ID=gene0;Name=BRESU_RS00010;gbkey=Gene;gene_biotype=protein_coding;locus_tag=BRESU_RS00010;old_locus_tag=Bresu_0001 (all in a single line)

NC_014375.1 Protein Homology CDS 273 1709 . + 0 ID=cds0;Parent=gene0;Dbxref=Genbank:WP_013267421.1;Name=WP_013267421.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_013267421.1;product=chromosomal replication initiator protein DnaA;protein_id=WP_013267421.1;transl_table=11 (all in a single line)

1) What should I type in the feature type box? The tutorial says to type "exon" corresponding to the third column of gff file in tutorial. However, I'm working with a bacterial genome and the third column is either "gene" or "CDS". What should I type in feature type box? 2) Also, the tutorial says to type "gene_id" in the ID attribute box. As shown above my gff file is different. So what should I type in there? In addition, I want to add attributes such as locus_tag, old_locus_tag and product for my final table after DESeq2.

Thank you.

rna-seq • 486 views
ADD COMMENTlink modified 7 months ago by Jennifer Hillman Jackson25k • written 7 months ago by adhikari_satish0
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson25k wrote:


You'll need to use GTF format with HTseq-count.

You annotation data is in GFF3 format, not GTF. Datatype FAQ with help/links to format specifications:

Try the too gffread to convert the data or check your data source, many offer both formats representing the same data.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 7 months ago by Jennifer Hillman Jackson25k
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