Diffbind issue
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mtsompana • 0
@mtsompana-8724
Last seen 6 weeks ago
United States

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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")

names(samples)

samples

# 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

plot(screening)

# Remove blacklisted sites

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

# 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

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

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