-
still a problem?
Is this still a problem for anyone? I wrote a very simple script to convert .vcf to .gff3 format, it has not been tested, but you could try it and modify it for your own use if you want.Leave a comment:
-
I have the same problem, and unfortunately I see you didn't have much luck in finding an answer... How did you fix it?Leave a comment:
-
Converting VCF to GFF (again)
Hi folks,
I know the question was already asked here (as in http://seqanswers.com/forums/showthr...hlight=gff+vcf)..
But my problem is that the data I have are on plants, and are massive... I mean, I have performed a GATK SNP calling for ALL sites, including indel, and the final file is of 49Go (VCF).
My aim is to convert it to GFF, and in this GFF to include the large deletions (missing regions in queries either from non-existing sequence or from technical aspects) as well as the small SNP and indel. Moreover I would like to conserve the RG infos as I have multiple samples in the VCF
I wonder if someon already starts working on something like that ?
Thanks
Francois
-
At the intersection of cytogenetics and genomics lies the exciting field of cytogenomics. It focuses on studying chromosomes at a molecular scale, involving techniques that analyze either the whole genome or particular DNA sequences to examine variations in structure and behavior at the chromosomal or subchromosomal level. By integrating cytogenetic techniques with genomic analysis, researchers can effectively investigate chromosomal abnormalities related to diseases, particularly...09-26-2023, 06:26 AM -
Cancer research has been transformed through numerous molecular techniques, with RNA sequencing (RNA-seq) playing a crucial role in understanding the complexity of the disease. Maša Ivin, Ph.D., Scientific Writer at Lexogen, and Yvonne Goepel Ph.D., Product Manager at Lexogen, remarked that “The high-throughput nature of RNA-seq allows for rapid profiling and deep exploration of the transcriptome.” They emphasized its indispensable role in cancer research, aiding in biomarker...09-07-2023, 11:15 PM -
Ribonucleic acid (RNA) represents a range of diverse molecules that play a crucial role in many cellular processes. From serving as a protein template to regulating genes, the complex processes involving RNA make it a focal point of study for many scientists. This article will spotlight various methods scientists have developed to investigate different RNA subtypes and the broader transcriptome.
Whole Transcriptome RNA-seq
Whole transcriptome sequencing...08-31-2023, 11:07 AM
Leave a comment: