Question: Reference annotation file contains only transcript and CDS information, how to analyze the different expression of genes?
gravatar for zoukai3412085
6 months ago by
zoukai34120850 wrote:

hello, everyone,

My reference annotation gff file, which was downloaded from gigaDB(, contains only transcript ID and CDS information like this:

[root@xueduanliu Ginkgo_RNA_sequencing_analysis]# cat Ginkgo_biloba.gff | head -n 10

C24882126   Cufflinks    mRNA   33       1196      .      +         .          ID=Gb_00001;

C24882126   Cufflinks    CDS       33       116        .      +        0          Parent=Gb_00001;

C24882126    Cufflinks    CDS     219      460        .      +        0          Parent=Gb_00001;

C24882126    Cufflinks    CDS      542     863        .      +        1          Parent=Gb_00001;

C24882126    Cufflinks    CDS      945     1196      .      +        0          Parent=Gb_00001;

C24883216    EST             mRNA  236     1243     .       +        .           ID=Gb_00002;

C24883216    EST             CDS      236     1243     .       +        .           Parent=Gb_00002;

There is no exons and splice sites information in this reference annotation gff file, so how can I use to build hisat2 index and  map to genome by hisat2 and stringtie? 

tophat pipeline: Bowtie2 uses reference genome to build index then tophat uses  reference annotation file and samples' fastq file to map

hisat2 pipeline: hisat2 uses  reference genome and reference annotation file to build index then use samples' fastq file to map

My purpose is just to quantify genes in the reference annotation file, and then to analyze the different express of them, how can i do now?

ADD COMMENTlink written 6 months ago by zoukai34120850


Not sure this questions fits this forum as it is not directly related to bioconductor. You are more likely to receive help if you post names of the actual packages in bioconductor that you are trying to use or if it is a non-bioconductor question turn to biostars or other more general bioinformatic forums instead.

ADD REPLYlink written 6 months ago by thokall100
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