Bowtie Indices Unusually Large?
i'm making a bowtie index with bowtie-build 0.12.9, 64bit for hg19 obtained from UCSC using the standard 25 chromosome files (including chrY, chrM. The index I get is still being made but already exceeds 7 GB in size whereas the bowtie index for hg19 is only 2.7 GB (http://bowtie-bio.sourceforge.net/manual.shtml). Is this normal? Why is the posted index so much smaller? thanks.
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That seems a bit strange. Can I ask why you are re-indexing hg19 instead of using their pre-made index?
Can you post the full
bowtie-buildcommand you entered? It's hard to guess without that, though if I were forced to guess I'd say you accidentally gave it duplicate fasta files or something like that.There is not much I can see that could increase the index size except the
-Boption, which builds both letter and colorspace indexes.