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I'm not sure this is an 'issue' but I recently updated to a newer kallisto (and gencode reference) and noticed that the index files are 5 times smaller which made me wonder if I have mangled something.
Later gencode is larger as expected:
370M gencode.v31.transcripts.fa
585M gencode.v47.transcripts.fa
But resulting index is much smaller:
3.0G gencode.v31.transcripts.kallisto_0.46.0.idx
624M gencode.v47.transcripts.kallisto_0.50.1.idx
Just curious if you found a way to greatly improve the efficiency of storing the index? The mapping rates seem similar. The only notable difference is that I simplified fasta sequence names to remove some uninformative info.
I'm not sure this is an 'issue' but I recently updated to a newer kallisto (and gencode reference) and noticed that the index files are 5 times smaller which made me wonder if I have mangled something.
Later gencode is larger as expected:
370M gencode.v31.transcripts.fa
585M gencode.v47.transcripts.fa
But resulting index is much smaller:
3.0G gencode.v31.transcripts.kallisto_0.46.0.idx
624M gencode.v47.transcripts.kallisto_0.50.1.idx
Just curious if you found a way to greatly improve the efficiency of storing the index? The mapping rates seem similar. The only notable difference is that I simplified fasta sequence names to remove some uninformative info.
e.g.
became
I can't see how this would lead to a decrease in index size of 5-fold though.
thanks for reading!
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