User: Gordon Brown

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Gordon Brown70
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Posts by Gordon Brown

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Comment: C: DiffBind - error in dba.count
... Hi, I originally intended to include SAM support, but never got around to it. One of these days I will (or maybe just take it out of the documentation!). Cheers, - Gord From: António Miguel de Jesus Domingues > To: Gord Brown > Cc: "bioconductor@r-project.org" > Subject: Re: [BioC] Di ...
written 7.0 years ago by Gordon Brown70
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Answer: A: DiffBind - error in dba.count
... Hi, Ant?nio, DiffBind doesn't read SAM format, only BAM and (gzipped or uncompressed) BED. Try converting your SAM files to BAM. Cheers, - Gord P.S. "chr, start, end, score" isn't technically a legal bed file. You'd need "chr, start, end, NAME, score" for it to be a bed file. Though DiffBind ...
written 7.0 years ago by Gordon Brown70
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Comment: C: DiffBind - overlap between different peak callers
... Hi, Paolo, If it's crashing in dba.count, it either can't find the bed files of the reads, or doesn't like their format. Most likely the latter. One unfortunate restriction the release version has is that it expects bed files to have either exactly 3 or 6 (or more) columns. If your bed files hav ...
written 7.1 years ago by Gordon Brown70
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Answer: A: DiffBind error loading dba.count
... Hi, Paolo, 6Gb ought to be enough. I suspect there's something else wrong. Unfortunately, I don't have a Windows machine available to test on. Can you provide any other information about the error? Does it run for a long time, then fail, or does it fail quickly? Is there any other diagnostic mes ...
written 7.1 years ago by Gordon Brown70
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Answer: A: DiffBind error loading dba.count
... Hi, Paolo, DiffBind uses quite a lot of memory for the dba.count step, because it loads the whole data file into memory. (In hindsight, not the best design choice...) Try running with parallelization turned off: > test=dba.count(test,bParallel=F) so that it only loads one file at a time, to ...
written 7.1 years ago by Gordon Brown70
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Answer: A: DESeq - ChIP-seq (including background reads)
... Hi, Ian, You might consider using DiffBind, which wraps DESeq (and EdgeR) into a set of tools designed for ChIP differential binding. The vignette includes some examples of differential binding analyses. The use of replicates and input or background samples is included. It's part of Bioconductor ...
written 7.6 years ago by Gordon Brown70
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Answer: A: Problem installing Rsamtools
... Hi, Kathryn, Your copy of libbam (libbam.a) is a static library, not a shared library (and you can't, in general, link to a static library when trying to make a shared library). If you compile the shared version of libbam ("make dylib" in the samtools package will create "libbam.so.1"), and put it ...
written 8.0 years ago by Gordon Brown70

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