Enter the body of text here

Code should be placed in three backticks as shown below

```#DiffBind version 3.2.4

library(DiffBind) getwd() setwd("/Users/tsompana/Box/6. PROJECTS/8. Justin.Fasting.Enzalutamide.ATAC-seq/3.DiffBind/3.DiffBind_csv_files")

Read csv file

samples = read.csv("Screening.csv", header=TRUE, sep=",")

names(samples)

samples

read peaksets using the "dba" DiffBind function and creates a DBA object

The peak score (prior to counting reads) is the score from the fifth column for bed, normalized to a 0.1 interval by dividing each score by the maximum score

screening = dba(sampleSheet = samples)

screening

head(screening$peaks[[1]])

plot(screening)

Remove blacklisted sites

screening = dba.blacklist(screening, blacklist = DBA_BLACKLIST_HG19, greylist = FALSE)

include your problematic code here with any corresponding output

calculate binding matrix with scores based on read counts (affinity scores) for every sample using dba.count and default settings

screening=dba.count(screening, bParallel = FALSE)

screening

please also include the results of running the following in an R session

[W::hts_idx_load2] The index file is older than the data file: /Users/tsompana/Box/6. PROJECTS/8. Justin.Fasting.Enzalutamide.ATAC-seq/3.DiffBind/1.FinalBam/008a_screening_S16.sorted.bam.bai [W::hts_idx_load2] The index file is older than the data file: /Users/tsompana/Box/6. PROJECTS/8. Justin.Fasting.Enzalutamide.ATAC-seq/3.DiffBind/1.FinalBam/002a_screening_S20.sorted.bam.bai [W::hts_idx_load2] The index file is older than the data file: /Users/tsompana/Box/6. PROJECTS/8. Justin.Fasting.Enzalutamide.ATAC-seq/3.DiffBind/1.FinalBam/008a_screening_S17.sorted.bam.bai [W::hts_idx_load2] The index file is older than the data file: /Users/tsompana/Box/6. PROJECTS/8. Justin.Fasting.Enzalutamide.ATAC-seq/3.DiffBind/1.FinalBam/060a_screening_S37.sorted.bam.bai [W::hts_idx_load2] The index file is older than the data file: /Users/tsompana/Box/6. PROJECTS/8. Justin.Fasting.Enzalutamide.ATAC-seq/3.DiffBind/1.FinalBam/060a_screening_S38.sorted.bam.bai [W::hts_idx_load2] The index file is older than the data file: /Users/tsompana/Box/6. PROJECTS/8. Justin.Fasting.Enzalutamide.ATAC-seq/3.DiffBind/1.FinalBam/002a_screening_S21.sorted.bam.bai [W::hts_idx_load2] The index file is older than the data file: /Users/tsompana/Box/6. PROJECTS/8. Justin.Fasting.Enzalutamide.ATAC-seq/3.DiffBind/1.FinalBam/002a_screening_S21.sorted.bam.bai [W::hts_idx_load2] The index file is older than the data file: /Users/tsompana/Box/6. PROJECTS/8. Justin.Fasting.Enzalutamide.ATAC-seq/3.DiffBind/1.FinalBam/008a_screening_S16.sorted.bam.bai [W::hts_idx_load2] The index file is older than the data file: /Users/tsompana/Box/6. PROJECTS/8. Justin.Fasting.Enzalutamide.ATAC-seq/3.DiffBind/1.FinalBam/002a_screening_S20.sorted.bam.bai [W::hts_idx_load2] The index file is older than the data file: /Users/tsompana/Box/6. PROJECTS/8. Justin.Fasting.Enzalutamide.ATAC-seq/3.DiffBind/1.FinalBam/060a_screening_S38.sorted.bam.bai [W::hts_idx_load2] The index file is older than the data file: /Users/tsompana/Box/6. PROJECTS/8. Justin.Fasting.Enzalutamide.ATAC-seq/3.DiffBind/1.FinalBam/008a_screening_S17.sorted.bam.bai [W::hts_idx_load2] The index file is older than the data file: /Users/tsompana/Box/6. PROJECTS/8. Justin.Fasting.Enzalutamide.ATAC-seq/3.DiffBind/1.FinalBam/060a_screening_S37.sorted.bam.bai sessionInfo( )

``` I am getting the warning messages above but the bai files were generated post bam. Could you please help me with this issue?