The link is right as you just posted it
When you download the sequence file you need to uncompress it: gunzip hs_ref_GRCh38.p12_chr20.fa.gz
Then, the command in the brief usage section of my original post analyse_DNA_sequence.pl --input-fasta hs_ref_GRCh38.p12_chr20.fa --ngram-length 3 --output-state hs_ref_GRCh38.p12_chr20.fa.3.state --output-stats stats.txt means the following:
- You are studying triplets of bases, e.g. ATC. This is the ngram-length = 3
- Once finished, the object holding the stats will be serialised to disk as hs_ref_GRCh38.p12_chr20.fa.3.state
- Brief info will be dumped to stats.txt
If you want to remember your findings from the first sequence file when you process a second and append new data to it, then you use the previously output ".state" file as input state (--input-state) for your new run. This is to allow processing gigabytes of sequences incrementaly in small batches.
bliako
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