Identifying full-length transcripts / adapter configuration
Closed this issue · 2 comments
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
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.
That's exactly what I was looking for! Thank you!