Creating Annotation GTF/GFF file
1
0
Entering edit mode
4 weeks ago
santos48 ▴ 30

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?

HG38 Annotation Rna-Seq Genome • 332 views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
ADD COMMENT
0
Entering edit mode

Is possible to annotated results %0 assigned using featureCounts?

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1586 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6