Help me with my GFFex results

Hallo dear community!

I'm new at bioinformatics, and recently used GFFex to extract intronic and intergenic regions. The question is, how do I validate these results? Anyone knows? Thanks a lot!

gff intron intergenic

• 1,945 views • link

updated 9.5 years ago by Biostar

• written 10.0 years ago by elfkatzenbr •

1 answer

You can validate a couple of these manually using a genome viewer such as IGV. You could also annotate your peaks using HOMER's annotatePeaks.pl or R's ChIPseeker.

• 1 views • link

written 10.0 years ago by Sinji

More posts like this

how to discover the dissimilar regions in alignment using pyhton?
written 4.5 years ago by m90 •

I'm doing comparison between two different strains of COVID-19 using Python , I did alignment using clustalw2 , Now i want detect the dissimilar regions …
blastn_vdb Error: Cannot open VDB:
written 4.9 years ago by Xavier •

I'm working locally with sra-toolkit. I have downloaded a sra files, validate it with `vdb-validate` and when I try to do a search with `blastn-dbd` …
How to extract intergenic regions
written 5.0 years ago by Ak •

I'm trying to obtain intergenic regions from the fasta file containing the genome sequence. I previously identified the exon-intron boundaries of a gene family (using …
How to extract reads/fragments aligned to intergenic regions from bam/sam file?
written 6.4 years ago by MACRODER •

Hi. I'm new to RNA-seq data analysis, and I'm trying to extract all reads/fragments aligned in intergenic regions from a sam/bam file. I have a …
High intronic mappings in the RNASeq
written 6.8 years ago by shangyuan5000 •

Hi, I have some samples from a frozen tissue bank, extract the RNA and sent them to RNASeq. The result mappings are weird to me, …
Lots of chip regions with high GC content and low sequence depth were detected
written 7.7 years ago by cginsea •

Dear All. In human genome panel sequencing, we found that some chip regions with high GC content were enriched in low sequence depth parts. So, …
find pseudogenes for a new genome annotation
written 8.7 years ago by qwzhang0601

Hello: Recently, we assembled a new rodent species and did the genome annotation. We found several gene families are under expansion in the new species. …
How to compute RNA-Seq mapping stats for rRNAs?
written 9.9 years ago by PAn •

Hi all, I have RNASeq aligned bam files from tophat for human samples and I need to find out the percent reads mapped to rRNA( …
How to validate a model obtained from Modeller
written 10.7 years ago by thaonguyen8310 •

I have some difficulties in reading result from Modeller. After obtaining the model from Modeller and use Gnuplot, I have a graph of model and …
RefSeq Genes on IGV
written 10.7 years ago by Bioradical •

I have recently been playing around with enhancer marks in intergenic regions versus intragenic regions and I have noticed that some of the intronic regions …