makeIndex: cannot open file about tagmeppr HOT 6 CLOSED

Hi,

Could you please add the code you used?

I'm thinking that you directly copied this code from the vignette:

reference_hg19_PB = makeIndex(indexPath = '../premadeReferences/',
                         bsgenome = BSgenome.Hsapiens.UCSC.hg19,
                         ITR = 'PiggyBac',
                         targetInsertionSite = 'TTAA', verbose = T)

Can you confirm that there is a folder called premadeReferences at the right place? Try this:

dir.exists('../premadeReferences/')

from tagmeppr.

Yes, I copied the code from the vignette assuming that the imported library ("BSgenome.Hsapiens.UCSC.hg19") would have a premadeReferences folder.
dir.exists('../premadeReferences/') shows that there is no such folder.

from tagmeppr.

I see. If you are in your preferred working directory (you can test this with getwd()), you can easily make the other directory with dir.create("premadeReferences") as a subdirectory of the one you are in now.

from tagmeppr.

I assume that you have BWA installed.

from tagmeppr.

Thanks,
I was able to map insertions in a mouse ES cell clone of our interest using the code. Will it be possible to continue this thread or a new thread of discussion on these two issues:

1. using a different p value as a cut-off?
2. using T2T genome assembly for aligning human genome reads? The "BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0" version needs R "4.2", but tagmeppr is not availble for this R version 4.2.

from tagmeppr.

Great to hear. Yes, please make new issues for those two questions.

from tagmeppr.