Help with error makeTxDbFromGFF in GenomicFeatures package

Question

[Chris]

Hi all,

Would you have a suggestion for the error below? Thank you so much.

txdb <- makeTxDbFromGFF(opt$gtf)

Error in .detect_file_format(file) : Invalid 'file'. Must be a path to a file, or an URL, or a connection object, or a GFF3File or GTFFile object.

opt $cores [1] 1

$help [1] FALSE

I am trying to follow the codes here to annotate Grange object created from DiffBind but not sure if the input for the list function below correct:

https://github.com/jianhong/atacseq/blob/master/bin/diffbind.r

option_list <- list(make_option(c("-d", "--design"), type="character", default=NULL, help="samplesheet_DiffBind.csv", metavar="path"),
                    make_option(c("-p", "--peaks"), type="character", default=NULL, help="peak files", metavar="string"),
                    make_option(c("-g", "--gtf"), type="character", default=NULL, help="Homo_sapiens.GRCh38.107.gtf", metavar="path"),
                    make_option(c("-b", "--blacklist"), type="character", default=NULL, help="hg38-blacklist.v2.bed", metavar="path"),
                    make_option(c("-s", "--species"), type="character", default=NULL, help="species", metavar="string"),
                    make_option(c("-c", "--cores"), type="integer", default=1, help="16", metavar="integer"))

[rpolicastro]

Replace opt$gtf with a path to your GTF file such as "/file/path/genome.gtf" If you're processing this in the R interpreter instead of running this on the command line and providing those options as arguments to the script.

[Chris]

I tried that before seeing your suggestion but I saw the infinity sign when running so not sure if that is correct. Thank you for your reply!

[rpolicastro]

If it's a large gtf and/or compressed it might take a minute or two to load. I would give it some time and see if it completes.

[Chris]

Could I ask a follow up question about the output of annotatePeakInBatch() below?