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Answer: how to use Rsamtools to parse extra fields from STAR alignment
by
Martin Morgan
25k
The 'extra columns' are called 'tags' in the SAM specification. Following the documentation `?ScanBamParam` you should add `tag = "NH"`. Se…
Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip
by
Delta._.43
▴ 10
Yes, indeed it is the same error. Here are the first few lines of my count file. ``` "ENSG00000000003":"001" 0 "ENSG00000000003":"002" 1032…
Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip
by
Alejandro Reyes
★ 1.8k
Thanks for your detail post. I think this might be related to this issue here: https://support.bioconductor.org/p/9143537/ Just to verify…
Answer: spot- vs cell-level data access
by
Leonardo Collado Torres
▴ 980
Hi, The `SingleCellExperiment` object you can download with `fetch_data(type = "sce")` pre-dates the creation of `SpatialExperiment`. No…
Answer: unable to install.packages("spatialLIBD")
by
Leonardo Collado Torres
▴ 980
Hi @kstern, Thank you for your interest in `spatialLIBD`. You will still need the package in order to re-cast the object into a `Spatia…
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error running UniProt.ws
Answer: DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FU
C: No genes found in universe : goana error
A: No genes found in universe : goana error
No genes found in universe : goana error
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