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

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?

DiffBind • 57 views
ADD COMMENT

Login before adding your answer.

Traffic: 276 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6