I am trying to convert single-cell ATAC-seq regions to their overlapping gene values using promoter regions and gene information. I am following this tutorial, but I cannot generate the final feature matrix. I appreciate if you have any suggestions.

I have used bedmap to get overlap between my fragments.bed and genes.bed file as follows:

bedmap --ec --delim "\t" --echo --echo-map-id genes.sort.bed fragments.sort.bed > atac_genes_bc.bed

Some information about my files:

head genes.sort.bed

chr1    10868   12368   DDX11L1     .   +
chr1    16935   18435   MIR6859-1   .   -
chr1    28553   30053   MIR1302-2HG .   +
chr1    29069   30569   WASH7P.     .   -
chr1    29365   30865   MIR1302-2   .   +

head fragments.sort.bed #single-cell ATAC-seq data; last column is the value in the open chromatin region for column 4's cell name.

chr1    191337  191587  AAAGTGCCACAT    1
chr1    191337  191587  AAATTCAGGCGG    1
chr1    191337  191587  ATCCTCTTACAT    1
chr1    191337  191587  CTCACCATACGG    1
chr1    191337  191587  GACGTTCAATCC    1

head -100 atac_genes_bc.bed | tail -5

chr1    1385710 1399338 NM_030937   0   -   1387230 1399306 0   11          1872,93,112,142,105,100,65,121,110,75,320,  0,2066,2243,4519,4748,5055,7685,9683,12522,12886,13308,     AACCCTGGCGGA;AACCTCACTATA;AATGCCAGACTA;ACAAATAACAGT;ACACTGAGCAGG;ACCGGTAGCTGA;ACTTGTTAGTCT;AGACGAATCTAA;AGTGAACCAGTG;AGTGAAGATGGC;ATCCTCTTACAT;ATGCGATCTCTG;ATTTGTTGAGCA;CAAAGGGCACTA;CAGCTGGTGATG;CAGTTACGAATG;CATCTTAATTAG;CCAACCGTAGAT;CCTGTGATAAGG;CGAGCTGTTATC;CTCAACCCATTG;CTGCGACACTGG;GAAATTTATTAG;GACGTATATGCC;GAGTCGCTAGGA;GAGTTGGGGATG;GATCTCCACAGG;GCGACGCCACCA;GCGCATATAAGT;GGCCACTTGCTG;GGTCTTTGTGCC;GTATCATTTGCA;GTCAGATTGCCT;GTGCTTATAGTC;TAAGCTCTTAAG;TACCAAAACATT;TAGGTCGGATAA;TAGTGTCTGGCG;TCATGAGTTCCG;TCCCCCTCGGCT;TGACCTGGATAA;TGCACCATATCA;TGCACTTCACAT;TGGACGCGCTTT;TTCATTATCTGC;TTCATTGAGCAT;TTCCTTTCGGTA;TTTTCCGCCACC
chr1    1392287 1399338 NM_001039577    0   -   1392781 1399306 0   6   516,65,121,110,75,320,  0,1108,3106,5945,6309,6731, AACCCTGGCGGA;AACCTCACTATA;AATGCCAGACTA;ACAAATAACAGT;ACACTGAGCAGG;ACCGGTAGCTGA;ACTTGTTAGTCT;AGACGAATCTAA;AGTGAACCAGTG;AGTGAAGATGGC;ATCCTCTTACAT;ATGCGATCTCTG;ATTTGTTGAGCA;CAAAGGGCACTA;CAGCTGGTGATG;CAGTTACGAATG;CATCTTAATTAG;CCAACCGTAGAT;CCTGTGATAAGG;CGAGCTGTTATC;CTCAACCCATTG;CTGCGACACTGG;GAAATTTATTAG;GACGTATATGCC;GAGTCGCTAGGA;GAGTTGGGGATG;GATCTCCACAGG;GCGACGCCACCA;GCGCATATAAGT;GGCCACTTGCTG;GGTCTTTGTGCC;GTATCATTTGCA;GTCAGATTGCCT;GTGCTTATAGTC;TAAGCTCTTAAG;TACCAAAACATT;TAGGTCGGATAA;TAGTGTCTGGCG;TCATGAGTTCCG;TCCCCCTCGGCT;TGACCTGGATAA;TGCACCATATCA;TGCACTTCACAT;TGGACGCGCTTT;TTCATTATCTGC;TTCATTGAGCAT;TTCCTTTCGGTA;TTTTCCGCCACC
chr1    1399529 1402046 NR_015434   0   +   1402046 1402046 0   3   160,146,1442,   0,628,1075, AACCCTGGCGGA;AACCTCACTATA;AATGCCAGACTA;ACAAATAACAGT;ACACTGAGCAGG;ACCGGTAGCTGA;ACTTGTTAGTCT;AGACGAATCTAA;AGTGAACCAGTG;AGTGAAGATGGC;ATCCTCTTACAT;ATGCGATCTCTG;ATTTGTTGAGCA;CAAAGGGCACTA;CAGCTGGTGATG;CAGTTACGAATG;CATCTTAATTAG;CCAACCGTAGAT;CCTGTGATAAGG;CGAGCTGTTATC;CTCAACCCATTG;CTGCGACACTGG;GAAATTTATTAG;GACGTATATGCC;GAGTCGCTAGGA;GAGTTGGGGATG;GATCTCCACAGG;GCGACGCCACCA;GCGCATATAAGT;GGCCACTTGCTG;GGTCTTTGTGCC;GTATCATTTGCA;GTCAGATTGCCT;GTGCTTATAGTC;TAAGCTCTTAAG;TACCAAAACATT;TAGGTCGGATAA;TAGTGTCTGGCG;TCATGAGTTCCG;TCCCCCTCGGCT;TGACCTGGATAA;TGCACCATATCA;TGCACTTCACAT;TGGACGCGCTTT;TTCATTATCTGC;TTCATTGAGCAT;TTCCTTTCGGTA;TTTTCCGCCACC
chr1    1401895 1407313 NM_017971   0   -   1402082 1407217 0   4   361,78,111,183, 0,3913,5013,5235,   AATCCCACTAAT;ACCGCTAGCGGA;ATTCGCAATGCT;CTGGGCTCTTTA;CTTTTCTATCTC;GACGTTCAATCC;GATAGGTCGCAC;GATCCCTTGTGG;GATTGGCCTCTC;GCAGTCTCGGAC;GCCGTACCGCCT;GGAGGATACTTA;GGGTCGATTGTT;GTCAGATTGCCT;GTGGAGCTGTAA;TAGGTAACTAGC;TTCATGCCATGT
chr1    1418419 1421444 NM_001145210    0   -   1419099 1421005 0   4   1130,541,209,312,   0,1632,2377,2713,   CGCGATACGGCG;GAACACTTGCGT;GAGTGGGGCCCT;GCTGGCCGTTGA;GTCACTGGTCGC;GTGACTTCAAAT;GTGGATGATCAC;TAAGAGGGCTAC

My goal is to use the LIGER package to integrate single-cell RNA-seq and ATAC-seq data, according to this tutorial. The problem is that when I run the following R commands I get an error:

Reading barcodes of cells from original sc ATAC-seq data where I extracted fragments.bed to convert ATAC-seq regions to overlapping gene values with promoter regions.

library(rliger)
atac <- read.table('chromatin_counts.tsv', sep = '\t', header = TRUE, as.is = TRUE)
genes.bc <- read.table(file = "atac_genes_bc.bed", sep = "\t", as.is = c(4,12), header = FALSE)
barcodes <- colnames(atac)
genes.counts <- makeFeatureMatrix(genes.bc, barcodes)

Error: Error in makeFeatureMatrix(genes.bc, barcodes) : Expecting a string vector: [type=integer; required=STRSXP].

Thank you in advance!