How are index files look like? about methylpy HOT 5 CLOSED

It is something like this

1	0
2	3438
#eof

The first column is chromosome name and the second column marks the position in the file for accessing the cytosine methylation data of the corresponding chromosome.

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After building the index, I got lots of files with the end of .bt2. They are all binary files.
The command I used is:

methylpy build-reference --input-files Oh43.pseudomolecules-v1.fasta --output-prefix Oh43 --num-procs 8

Is that correct?

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You are totally right. The .bt2 are bowtie2 index file. I was confused because there are also other types of index files.

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But when I try to map the reads, it says:
"/scratch/yz7799962/test/oh43/Oh43.pseudomolecules_index/Oh43_F" is not a Bowtie 2 index
Should I replace this folder as one of the following file:
Oh43_f.1.bt2
Oh43_f.2.bt2
Oh43_f.3.bt2
Oh43_f.4.bt2
Oh43_f.fasta
Oh43_f.rev.1.bt2
Oh43_f.rev.2.bt2

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What was your command?

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