Entering edit mode
7.6 years ago
Bioinformatist Newbie
▴
270
Hello,
I am trying to use ChromImpute to impute the data for the missing histone marks. According to the manual, if you don't have the input data at 25bp bin resolution, you can convert it by (input should be .begraph or .wig file):
java -mx4000M -jar ChromImpute.jar Convert ./INPUTDIR ./inputinfofile ./chrominfofile ./CONVERTEDDIR
Problem: I am converting one .bedgraph file, its header is:
track type=bedGraph
chr1 0 10102 0
chr1 10102 10152 1
chr1 10152 10163 0
chr1 10163 10213 1
chr1 10213 17464 0
The output I get after converting is all zero values.. header of converted data for chr9 is:
track type=wiggle_0 name=E116_input_observed
fixedStep chrom=chr9 start=1 step=25 span=25
0
0
0
0
I have also tried converting my .sam alignment file into .wig but no matter what option I try, I get the same output where every line in output (converted data) is 0.
If somebody has worked with this then kindly help me with this problem. Thank you.
My bad.. The problem was with the file extension. I was using *.bed as input while, while it should have been *.bedgraph.
Hello Bioinformatist Newbie!
We believe that this post does not fit the main topic of this site.
PO answered his own question
For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
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Dear Pierre,
I am unable to see how this post does not fit the main topic of this site. Indeed, it is a bioinformatics-related post, but If you say that as I was able to figure out the answer myself so you want to delete the post, then go ahead, I don't have any issue with it. I'm okay with whatever you decide is better for the community.
Thanks.
I'm sorry I did it wrong !I clicked the wrong button. let me reopen the question. But please, close it later if you where able to solve your problem.