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Why are you worried about the file size? If all the files are not right bowtie2 should complain.
BTW: That file is about that size in the HG19_UCSC version from iGenomes that I use.Leave a comment:
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bowtie2 index on igenomes
The hg19.3.bt2 index reference from iGenomes is only 4kb where as the other 5 .bt2 are 600-915MB. Is this right or should I re-download again? Thank you.
ftp://ftp.ccb.jhu.edu/pub/data/bowtie2_indexes/hg19.zip
total size of zip 3.2GB
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