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Identifying full-length transcripts / adapter configuration #68

Closed LynnLy closed 11 months ago

LynnLy commented 11 months ago

Is your feature related to a problem?

I have a sensitive application for which we want to be as confident as possible that we are only using full length transcripts.

Describe the solution you'd like

Is there a way to log/find out the adapter configuration (full length, single adapter, etc) for each individual read?

Describe alternatives you've considered

I can re-run vsearch externally but it would save a lot of time if the information was retained somewhere. Thanks!

Additional context

No response

nrhorner commented 11 months ago

Hi @LynnLy

Currently this information is in a file that is not copied to the user output directory. I should probably add that in an upcoming release.

In the meantime, you can locate this file by looking in <out_dir>/execution/trace.txt for the line containing pipeline:stranding:combine_adapter_tables which should look like this:

21 8f/a6c024 484342 pipeline:stranding:combine_adapter_tables (1) COMPLETED 0 2023-12-16 09:11:01.834 1.1s 28ms 93.5% 0 0 1 MB 553.2 K

The second column specifies the prefix to the relevant work directory. so in this case, you would look for the following file: <work_dir>/8f/a6c024.../<alias>_read_config.tsv, which contains the adapter configurations for each read.

LynnLy commented 11 months ago

That's exactly what I was looking for! Thank you!