comprna / r2dtool Goto Github PK

Hi team,

So I tried running the suggested R2Dtool. The CHEUI output file (site_level_5mC_prediction) looked like this:

The command bash cheui_to_bed.sh [cheui model II output file] [cheui_to_bed output file] created a file that looked like this:

For some reason it hasn;t copied the complete gene accession IDs. Probably the reason why Rscript ./scripts/R2_annotate.R ./test/out_CHEUI_modelII.bed ./test/GRCm39_subset.gtf ./test/out_CHEUI_modelII_annotated.bed gave the following error:

Please let me know what went wrong and how to proceed further.

Thank you for your response and efforts,

Sukriti

Hi,

When using the R2_lift.R script with GENCODE annotation file, I encounter the error with transcript_id.
`Problem with transcript_id.
Backtrace:

1. ├─... %>% mutate(score = ".", .after = metaname)
2. ├─dplyr::mutate(., score = ".", .after = metaname)
3. ├─dplyr::inner_join(mappedLocus, strand_lookup, by = "transcript_id")
4. └─dplyr:::inner_join.data.frame(mappedLocus, strand_lookup, by = "transcript_id")
5. └─dplyr:::join_mutate(...)

6. └─dplyr:::join_cols(...)
   

7.   └─dplyr:::standardise_join_by(...)
   

8.     └─dplyr:::check_join_vars(by$x, x_names, error_call = error_call)
   

9.       └─rlang::abort(bullets, call = error_call)
   

Execution halted
`
I follow your generate notes, commenting out line 25 in lift.R and line 27 in annotate.R. But it seems update, does not corresponding with it.
In addition, same error with test data.

Bai,
Thanks a lot