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.
A simple Python script to detect whether a string has Google Scholar result.
An annotation transfer stratagy between different geome assemblies using RATT, Augustus, blast and scripting.