ChIPpeakAnno toGRanges error

Question

[tarek.mohamed]

Dear All,

I am trying to use ChIPpeakAnno package to annotate peaks generated by MACS2. First, I tried to convert my peaks file to GRange object using toGRanges function. It did not work when I used summit.bed or .xls MACS2 files, however, it only worked with narrowPeak files. I need to use summit.bed file as it has more information.

>peaks_grange<-toGRanges("result_input_bowtie_q0.05_summits.bed",format="BED")

Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : scan() expected 'an integer', got 'HSCHR10_1_CTG3'

 >peaks_2<-toGRanges("result_input_bwa_q0.05_peaks.xls",format="MACS2")

Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : scan() expected 'an integer', got 'HSCHR10_1_CTG3'

> peaks<-toGRanges("result_input_bowtie_q0.05_peaks.narrowPeak" ,format="narrowPeak")

Warning message: In formatStrand(strand) : All the characters for strand, other than '1', '-1', '+', '-' and '', will be converted into ''.

Thanks Tarek

[Alex Reynolds]

Can you indicate what information (columns?) you need from summit.bed for annotation? Other toolkits may offer the features you need to solve your problem.

Answer 1

[BioinfGuru]

Sounds like chippeakanno parsing only allows the file structure of the summit.bed file