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tushiqi / MAnorm2_utils

To pre-process a set of ChIP-seq samples and coordinate with MAnorm2 for differential analysis
GNU General Public License v3.0
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MAnorm2_utils could not process the read file #3

Open maisarahabs opened 4 years ago

maisarahabs commented 4 years ago

Hi. I converted my bam files to sam. Then I used sam2bed.

I used the command profile bins for my peak files and read files; both were in bed format.

The tool could read the peak files but could not process the read files.

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Produced by profile_bins, version=1.0.0

Equivalent parameter settings: peaks=suz12_13CF.bed,suz12_14CF.bed reads=suz12_13.markdup.bed,suz12_14.markdup.bed labs=s13,s14 n=suz12 min-peak-gap=150 typical-bin-size=1500 summits=using_middle_points paired=True keep-dup=all method=byBin fix-bin-size=False

Summary of peak numbers in peak files: peak_file peaks_after_filtering peaks_after_merging suz12_13CF.bed 36694 36694 suz12_14CF.bed 38237 38237

Divide merged peaks into reference genomic bins: 77196 bins in total

Errors occur when parsing the read file, suz12_14.markdup.bed:

Program aborted.

Please advice. Thank you.

tushiqi commented 4 years ago

@maisarahabs Sincerely sorry for my late response. Typically it is because of the format of the read file. But it is indeed strange that the program has not printed any information about the specific problem. Could you please send me the read file so that I can track the progress of the program?

Thanks.