Hi
I have the same problem.
How can I replace Trinity gene numbers to real gene names ?
I have blast hits file from TransDecoder of Trinity.
My question is that how to run DEG to get real gene names, not the Trinity names (Tr1...Trn..)?
-
Answered my own question
Well, since this problem went unanswered, I figured out a way to resolve this issue. It involves all of the things I thought it might, and there may be a simpler way. If you have a better method, please reply so that your solution will be easy to find.
Solution:
bwa-mem of Trinity.fasta to reference genome
samtools -Sbh | bam2bed | bed12ToBed6 | bedToGenePred stdin stdout | genePredToGtf file stdin assembly.gtfLeave a comment:
-
How do I convert Trinity output to GTF/GFF?
Hello everyone and thank you for your time,
This is a reiteration of an unanswered question:
TRINITY:Input (Fastq) and Output files (GFF)
How can I convert (FASTA) transcripts produced from Trinity into a GTF/GFF file? I am not interested in alternative workflows for particular things, I just want a GTF/GFF annotation file. Also, I'm not familiar with any long sequence alignment algorithms (would BWA be best??) and a simple conversion to GTF/GFF. Can you please suggest a simple workflow?
-
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
Leave a comment: