User: zhenfeng.liu1

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Posts by zhenfeng.liu1

<prev • 6 results • page 1 of 1 • next >
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Is it possible to change how DiffBind merge peaks?
... The default behavior of DiffBind when merging peaks from different samples is that peaks with at least 1 bp overlap will be merged. For example, peak chr1:100-300 will be merged with peak chr1:299-500. Is it possible to change this behavior, for example, requiring at least 50% bp overlap between the ...
chipseq diffbind written 12 weeks ago by zhenfeng.liu110 • updated 9 weeks ago by Rory Stark3.0k
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Comment: C: Integer overflow issue with ChIPQC
... I haven't figured out what's wrong, but when I reverted back to version 1.18.2, the error went away. ...
written 4 months ago by zhenfeng.liu110
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Answer: A: ChIPQC gives Bam file has 297 contigs Error: subscript contains out-of-bounds in
... After some research, I think I've found the cause of this bug. In ChIPQC:::sampleQC function, there is code to check for read length with the first 1000 reads of the first chromosome. Code follows: if (k == 1) { tocheckforreads <- 1000 readlength = round(mean(width(temp[1:toc ...
written 4 months ago by zhenfeng.liu110
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Comment: C: ChIPQC gives Bam file has 297 contigs Error: subscript contains out-of-bounds in
... I am running into the same error. Did you figure out the cause of the error? ...
written 4 months ago by zhenfeng.liu110
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Comment: C: Integer overflow issue with ChIPQC
... I have the exact same error. It's strange that some BAM file will work, but other will not. Did you figure out how to fix this? ...
written 4 months ago by zhenfeng.liu110
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Comment: C: ATAC-Seq peaks quality control with ChIPQC package, but getting error
... Got the same error. Any resolution? ...
written 4 months ago by zhenfeng.liu110

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