level_sample_compare have different index name

[RainaYin-sys]

Hi,

My two samples have different index name and it report an error when I run the following command:

tombo detect_modifications level_sample_compare --fast5-basedirs ${sigle_fast5_base_dir}/A1.sigle_fast5 --corrected-group RawGenomeCorrected_000
--alternate-fast5-basedirs ${sigle_fast5_base_dir}/B1.sigle_fast5 --corrected-group RawGenomeCorrected_001 --minimum-test-reads 50
--processes 8 --statistics-file-basename A1vsB1.level_compare

[17:46:33] Parsing Tombo index file(s). ******************** WARNING ******************** Tombo index file does not exist for one or more directories. If --skip-index was not set for re-squiggle command, ensure that the specified directory is the same as for the re-squiggle command.

How can I set this command?

[SycamoreLeaf]

It sounds like you want to run level_sample_compare, but your .tombo.index files don't have the names that Tombo expects.

Tombo guesses the filepath of the index files based on the filepaths of the fast5 basedirs. Try copying your index files to

• ${sigle_fast5_base_dir}/.A1.sigle_fast5.RawGenomeCorrected_000.tombo.index
• ${sigle_fast5_base_dir}/.B1.sigle_fast5.RawGenomeCorrected_000.tombo.index

The index files are Python pickle objects; so if you know Python you can open them up and monkey around with them.

[marcus1487]

@Chris-Kimmel That is close, but I don't think that will work. Tombo uses that value to extract the corresponding data from the single FAST5 files. So just changing the name or even the data in the index will not help.

Tombo only allows comparison of datasets resquiggled with the same --corrected-group attribute.

This is one of many poor design decisions made in Tombo. We have been hard at work internally on a complete redesign of Tombo and hope to release this software soon, though we do not have a specific date at this time.