Skip to content

Error wtih get_merge_fasta #12

Description

@thangnx1012

Hi, Great tools.

I got stuck at the merge_fasta step, where I used data from your tutorial: https://jiang-junyao.github.io/IReNA/bulk-ATAC+scRNA#integrate-bulk-atac-seq-and-scrna-seq-data-to-reconstruct-regulatory-networks

filtered_footprints <- read.table(file.path(analysis_dir, "ATAC-seq", 'footprints.bed'),sep = '\t')

fastadir <- file.path(analysis_dir, "Genome")
merged_fasta <- get_merged_fasta(filtered_footprints, fastadir)
Warning in merge_footprints(footprints, ditance = distance) :
NAs introduced by coercion
Error in pva1 + pva2 : non-numeric argument to binary operator

###merge footprints whose distance is less than 4
filtered_footprints <- read.table(file.path(analysis_dir, "ATAC-seq", 'footprints.bed'),sep = '\t')
fastadir <- file.path(analysis_dir, "Genome/hg38.fa")
merged_fasta <- get_merged_fasta(filtered_footprints, fastadir)
Error in validInput(fastadir, "fastadir", "direxists") :
Input value for 'fastadir' is not a direxists, (fastadir = character) please supply valid input!

Could you help me out with this issue?
Thank you!

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions