Is indexing a genome the same as annotating a genome?
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2.6 years ago
ATCG ▴ 370

Is indexing a genome the same thing as creating annotations?

For example, in Samtools we use the index option with a genome.fasta and transcripts.fasta and the output is a bam file does this file contain annotations? If so, is this bam file similar to a .gtf or .gff file?

Thanks!

samtools index genome indexing • 633 views
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GenoMax 123k

No. Indexing is a procedure used to facilitate fast random access in sequence/index files.

Genome annotation on other hand is a process where we identify location of coding exons, introns and other genomic features, which leads to creation of gene models that then get encoded in GTF/GFF files.

BAM files do not contain annotations.

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