I am using RSEM (with bowtie2) for alignment then gene count. Using Refseq Annotation (gff3), and genomic.fna reference Fasta file from NCBI. RSEM can convert gff3 to gtf file.
How can I subset the GTF file (or gff3 file) by gene a name. I want to extract the annotation (gtf) for particular gene and extract the gene sequence from reference Fasta file. Then I want to perform alignment.
This is especially to reduce time by avoiding aligning whole genome.
Thanks in anticipation.