I usually extract out fasta sequences using samtools:
i.e to extract the sequences for gene 000001
samtools faidx /path/to/transcriptome 000001
However, I was wondering whether there was a better method for extracting isoform sequences. I have tried the following command, but to no avail, to extract the sequences for gene isoforms 000001.1, 000001.2, 000001.3:
samtools faidx /path/to/transcriptome 000001.*
Does anyone have any tips on how to do this effectively?