Currently I am using DiffBind for a project of my Bioinformatics study in Leiden, The Netherlands.

I am trying to run the followings commands in R as shown in the "Example: Obtaining differentially bound sites" 

steps of the manual:  

(https://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf)

> library(DiffBind) 

> setwd(system.file("extra", package="DiffBind")) 

> tamoxifen <- dba(sampleSheet="tamoxifen.csv") 

> tamoxifen <- dba.count(tamoxifen) 

> tamoxifen <- dba.contrast(tamoxifen)

> tamoxifen <- dba.analyze(tamoxifen) 

> tamoxifen.DB <- dba.report(tamoxifen) 

The command for reading in the samplesheet is working, but when I try to make the counts I get 16 warnings and an error for not accessible files.

Warning messages:

1: reads/Chr18_BT474_ER_1.bam not accessible

2: reads/Chr18_BT474_ER_2.bam not accessible

3: reads/Chr18_MCF7_ER_1.bam not accessible

4: reads/Chr18_MCF7_ER_2.bam not accessible

5: reads/Chr18_MCF7_ER_3.bam not accessible

6: reads/Chr18_T47D_ER_1.bam not accessible

7: reads/Chr18_T47D_ER_2.bam not accessible

8: reads/Chr18_TAMR_ER_1.bam not accessible

9: reads/Chr18_TAMR_ER_2.bam not accessible

10: reads/Chr18_ZR75_ER_1.bam not accessible

11: reads/Chr18_ZR75_ER_2.bam not accessible

12: reads/Chr18_BT474_input.bam not accessible

13: reads/Chr18_MCF7_input.bam not accessible

14: reads/Chr18_T47D_input.bam not accessible

15: reads/Chr18_TAMR_input.bam not accessible

16: reads/Chr18_ZR75_input.bam not accessible

> tamoxifen <- dba.count(tamoxifen)

Error in pv.counts(DBA, peaks = peaks, minOverlap = minOverlap, defaultScore = score,  : 

  Some read files could not be accessed. See warnings for details.

In addition: There were 16 warnings (use warnings() to see them)

I have looked in the map of DiffBind in R but can't find any directory called "reads".

Am I looking in the wrong folder or do I have to download this specific directory elsewhere?

If anyone could give me further information, that would be very helpful. 

Hi Bob-

The data for the vignette, including the bam files, are available for download from this page:

http://DiffBind.starkhome.com

unzip and untar the file at the "Vignette Data: ER binding in tamoxifen resistant and responsive cells (chr18 only)" link, make this your working directory, and you can run all the steps of the vignette, including the dba.count() ones.

There is a footnote in the vignette at the point of the first call to dba.count() mentioning this, and referring to Section 8: Vignette Data, which includes these instructions as well.

Cheers-

Rory

Hey Rory,

Thank you so much for the solution!

Best regards,

Bob

The link can be found on this page with a variety of DiffBind resources.

The data link is currently: https://content.cruk.cam.ac.uk/bioinformatics/software/DiffBind/DiffBind_vignette_data.tar.gz