run via command line?

[jthomas5062]

Hello, is it possible to run EditR via command line via e.g., passing the gRNA sequence and the .ab1 as input?

[MitchellKluesner]

Hi James,

I have not yet written a version of the program that can be ran through the command line, however if you are looking for a barebones analysis the script run_for_ngs might be of use. This script from our follow up publication can take the same inputs and return a list of tibbles with all relevant information, besides the chromatogram. I've modified the script before to run through an apply statement for batch analysis.

Because Sanger sequencing is often noisy, I've found it to be best to look at every file manually to assess reliability, as such I haven't invested much time in developing a command line tool for EditR. However, I know that this is a common question so it might warrant we revisit this application.

Let me know how else I can be of help,

Mitch

[jthomas5062]

Hi Mitch, thanks a bunch for the quick reply. I agree that it's worth while taking a look at the data given the noise. That said, it would be helpful to be able to run all of the data quickly (i.e., when I have >several hundred sanger traces) just to get a sense of what is going on :) Thanks again!

[jthomas5062]

Mitch, sorry, but can you provide an example of how to run "run_for_ngs" on an example sanger file? e.g., providing gRNA sequence and .ab1 file as input?

[MitchellKluesner]

Hey James! Still working on this, let me give you an update tomorrow on where I'm at with making a barebones batch version of the software.

[jthomas5062]

Thanks a bunch for working on this Mitch! Of course, no rush :)

[jthomas5062]

Hi Mitch, wanted to check in to see if there were any updates on this? Thanks a million!

[MitchellKluesner]

Hi James! Sorry for the delay as I've been on vacation and still recovering from an illness.

I'm still working on this, but I hope to send you a barebones version by the end of the day!

Mitch

[jthomas5062]

Yikes -- sorry to hear that! Hope you are feeling better and of course no rush :). Thanks a bunch!

[MitchellKluesner]

Hi James!

Here is v1.0.0. The entire directory should allow for a reproducible analysis. The README.txt has instruction, however fair warning there is virtually no error handling so there will probably be some debugging involved. Let me know what issues come up!

Mitch

[jthomas5062]

Amazing -- thanks a ton, Mitch. I will keep you posted re: any unexpected issues :)

[jthomas5062]

Hey Mitch, sorry, just now getting around to trying this out. Do you have the "pre_trinucleotide_table.tsv" file that you could provide. I'm getting an error when sourcing global.R. Thanks!

[jthomas5062]

Ah, actually, I realized that this file isn't necessary :)

[M27Lewis]

Hi Mitch, I'm collaborating with James and have recently been testing out the EditRBatch you provided. Thank you so much! We have it working with several of our test input files and it is so helpful! I was wondering if there was a way to lock the sgRNA sequence as a reference for the analysis and chromatograms so that the target base number in the output is based on its location in the provided sgRNA sequence. Right now it seems to shift the location so that the first base is one of the specified edited bases, which changes the target base number sometimes. Would that be possible? Thanks again!

Mike

[M27Lewis]

Hi Mitch, following up on an error we're encountering with the EditRBatch. A lot of our files work fine, but several results lead to this error and we've been troubleshooting to determine why certain files are failing, but can't find any clear difference/problem. Do you have any insight why this error might be popping up? We really appreciate any suggestions or tips that will shed some light on how to address this. Thanks!

processing file: EditRBatch.Rmd |................................ | 62% [unnamed-chunk-4] Quitting from lines 96-109 [unnamed-chunk-4] (EditRBatch.Rmd) Error in names(motif_positions) <- rep(x = c(1:n_alignments), each = nchar(motif)): ! 'names' attribute [50] must be the same length as the vector [0] Backtrace:

1. BiocGenerics::lapply(...)
2. base::lapply(X = 1:nrow(params.tbl), FUN = runEditRBatch, params = params.tbl)
3. global FUN(X[[i]], ...)
4. global runEditR(...)
5. base::suppressWarnings(...)
6. base::withCallingHandlers(...)

Execution halted