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gagneurlab / drop

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
MIT License
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Can't load fds-object from DROP in R #555

Closed mmartinezj closed 3 months ago

mmartinezj commented 3 months ago

Hi, I have tried to load the fds object obtained from DROP run (aberrantSplicing module) in order to modify the plots from Overview.R, but when I try to load the object, this error arises:

error_loading_fds

I have tried to load the fds-object from the DROP demo run, and I could load it without any problem. I have tested this with FRASER v1.99.4 on R.

Thanks in advance!

Miriam

Update: checking the scripts used for DROP pipeline, I found a line on the 01_0_countRNA_init script: strandSpecific(fds) <- colData(fds)$STRAND. When I ran it, the error was the following Error in switch(tolower(value), no = 0L, unstranded = 0L, yes = 1L, stranded = 1L, : EXPR must be a length 1 vector On my annotation file, on the STRAND column I used the reverse option, but it doesn't appear on the options of the error. I don't know if this might be the problem or might help!

AtaJadidAhari commented 3 months ago

Hi Miriam,

this is probably due to the changes in FRASER from v1.99.3 to v1.99.4. I suspect you have done your analysis with DROP v1.3.4 which uses FRASER v1.99.3 and probably saved fds-object with that version. Can you please try to load the fds-object with FRASER v1.99.3?

Best,

Ata

mmartinezj commented 3 months ago

Hi Ata, I did the analysis with DROP v1.4.0, tried to load it with FRASER v1.99.3 and got again the same error. I tried to reinstall v1.99.4 and after this reinstalation, I was able to load the fds-object. Probably something went wrong on the previous installation and that's why it wasn´t working. Thanks for the response!

Best,

Miriam