How to change the treatment_file-W200-G600-islands-summary file to the standard bed file format?

[danli349]

Hello:

How can I change the treatment_file-W200-G600-islands-summary file to the standard bed file format?

> library(ChIPpeakAnno)

> KDM6A <- toGRanges("peaks/4934_Cre_ChIP_KDM6A_mm10_ec_yeast.bam-W200-G600-increased-islands-summary-FDR0.01",
+                   format="BED", header=FALSE)
duplicated or NA names found. Rename all the names by numbers.
Error in df2GRanges(data, colNames, format, ...) : 
  This is not a standard BED file. Maybe it is narrowPeak or broadPeak
In addition: Warning message:
In formatStrand(strand) : All the characters for strand, 
            other than '1', '-1', '+', '-' and '*', 
            will be converted into '*'.

Thanks

[JasonJiangs]

Hello:

How can I change the treatment_file-W200-G600-islands-summary file to the standard bed file format?

> library(ChIPpeakAnno)

> KDM6A <- toGRanges("peaks/4934_Cre_ChIP_KDM6A_mm10_ec_yeast.bam-W200-G600-increased-islands-summary-FDR0.01",
+                   format="BED", header=FALSE)
duplicated or NA names found. Rename all the names by numbers.
Error in df2GRanges(data, colNames, format, ...) : 
  This is not a standard BED file. Maybe it is narrowPeak or broadPeak
In addition: Warning message:
In formatStrand(strand) : All the characters for strand, 
            other than '1', '-1', '+', '-' and '*', 
            will be converted into '*'.

Thanks

Hi, sorry for the late reply. We'd like to suggest you to use the bed file output after FDR control instead of this one, because the island summary output will include more information comparing to the bed format.