User: csoneson
csoneson • 100
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Posts by csoneson
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... We have done some investigations into quantification of nanopore data using several different approaches (including Salmon, Wub and featureCounts, based on minimap2 alignments): https://www.biorxiv.org/content/10.1101/574525v1. We noted that in many cases it can be difficult to unambiguously attribu ...
written 14 days ago by
csoneson • 100
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... As Hans-Rudolf already mentioned, changing the QuasR alignment parameters for bisulfite data is not recommended. Regarding the error, what other parameter combinations did you try to conclude that you "always get the following error [...] no matter what the parameters are"? I can reproduce this erro ...
written 4 months ago by
csoneson • 100
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Comment:
C: Kallisto output with DEXSeq
... You can do round(counts) to get a matrix of integers. Also note that if you previously did differential gene expression analysis with DESeq2, your count matrix is probably on the gene level. For DEXSeq, you need a transcript-level count matrix (i.e., by setting txOut=TRUE in the tximport call).
...
written 7 months ago by
csoneson • 100
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Comment:
C: Kallisto output with DEXSeq
... One option is to import the kallisto output into R with tximport (set txOut=TRUE to get the transcript-level count matrix). Then you can use DEXSeqDataSet() to create the DEXSeqDataSet object. You'll need to provide the featureID (which would be the rownames of the count matrix) and the groupID (whi ...
written 7 months ago by
csoneson • 100
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Comment:
C: tximport returns NA counts
... True, but that was only for 50 cells, for which txOut=FALSE also worked, so I guess it is not yet clear whether there is a set of cells for which txOut=TRUE works but txOut=FALSE doesn't.
...
written 18 months ago by
csoneson • 100
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Comment:
C: tximport returns NA counts
... I wonder if this could have to do with the automatic determination of the column types by read_tsv. By default I think it uses the first 1,000 values to determine the column type, and if these values are all 0 it may try to read the whole column as integers. This caused problems for me once (albeit ...
written 18 months ago by
csoneson • 100
0
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... Hi Vlad,
thanks for your reply. I tried both your suggestions (I set OMP_FLAG="--disable-openmp" on line 96 in the configure file, my line 62 is about gcc), reinstalled lpsymphony and IHW from source, started new sessions, but unfortunately IHW still uses all the available cores on the machine. I'l ...
written 19 months ago by
csoneson • 100
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... Hi,
when I run IHW on our server it uses lots of computational resources (at least 20 cores). I can't seem to find any way to modify this in the call to ihw(). Is there a way to reduce the number of cores used by IHW?
Thanks!
Example code (from the IHW package) and session info:
library(IHW)
X ...
written 19 months ago by
csoneson • 100
• updated
19 months ago by
vladislav.kim • 10
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For C: Is it appropriate to use DESeq2 to analyse MinION data that's been mapped to a t
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