Question: ChIPpeakAnno toGRanges error
0
gravatar for tarek.mohamed
2.5 years ago by
tarek.mohamed250
tarek.mohamed250 wrote:

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

ADD COMMENTlink modified 2.5 years ago by YaGalbi1.4k • written 2.5 years ago by tarek.mohamed250

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.

ADD REPLYlink written 2.5 years ago by Alex Reynolds29k
1
gravatar for YaGalbi
2.5 years ago by
YaGalbi1.4k
Biocomputing, MRC Harwell Institute, Oxford, UK
YaGalbi1.4k wrote:

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

ADD COMMENTlink written 2.5 years ago by YaGalbi1.4k
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