I have a bed file that containing all Isoseq reads and I would like to remove those overlapped with multiple genes in the annotation file.
I was trying to build genometools on my Mac laptop accoring to the INSTALL instructions but with no success.
The are more and more RNAseq experiments coming out everyday. Data can be reused and meta-analysis can give more information. Here I list commonly used pipelines and tools.
Use Python (BioPython and gffutils) to extract sequences for gene features.
Notes on eukaryotic genome annotation.
In practice this is used to replace all IDs in a GFF file with your desired IDs, e.g. g10 to Smp_300010 but also g10.t1 to Smp_300010.1 (without 't').
Different ways to generate sequential numbers / ids, including using Excel, Vim, and shell command.
A collection of bioinformatics one-liners that I used quite often.