Creating Annotation GTF/GFF file

Question

[santos48]

Hello everyone, I have human Rna-Seq data reading by MiniOn.I aligned with the human reference genome (GRCh38.p13) from that website= https://www.gencodegenes.org/human/ using minimap2. Then I extract specific regions on the bam file using samtools. For the starting DESeq2, I tried to featureCounts with reference annotation folder bam file %5 assigned according to multiqc report.

How to create an annotation folder for quantification?

[Zhilong Jia]

Then I extract specific regions on the bam file using samtools.

why extract specific regions were used?

For the starting DESeq2, I tried to featureCounts with reference annotation folder bam file %5 assigned according to multiqc report.

unclear.

[santos48]

I extracted specific regions because of those regions I will research. I have noisy data that's why I extracted and annotated it. Then I checked results with multiqc in the results, samples assigned just %5.

[Zhilong Jia]

as you used only a subset of the genome, the 5% mapping rate is possible, regardless of the contaminated data.

Answer 1

[Zhilong Jia]

gene annotation gtf file

[santos48]

Is possible to annotated results %0 assigned using featureCounts?

[Zhilong Jia]

Yes, depends on actual reads which can be mapped to this region.