User: bruce.moran

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bruce.moran420
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Posts by bruce.moran

<prev • 98 results • page 1 of 10 • next >
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Comment: C: So frustrated compiling necessary packages in a linux system
... You can build Singularity containers as Ubuntu, CentOs, BioLinux etc. The underlying OS kernel might have some impact on versions you can run (e.g. don't think you can run CentOs7 container on a CentOs5 machine). ...
written 12 weeks ago by bruce.moran420
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Comment: C: So frustrated compiling necessary packages in a linux system
... [Singularity][1] is a '[container][2]', which is basically a portable computing environment. I think of it like a virtual machine, but at a software level. Containers are built based on 'recipes' which define the environment, including setup of all libraries, software, tools, reference data etc. jus ...
written 12 weeks ago by bruce.moran420
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Comment: C: So frustrated compiling necessary packages in a linux system
... Second this, and add that with VM you can run Linux OS on any local machine and so have access to root. Then test/build your Singularity recipe there, upload and pull from Singularity-Hub as user. Such a good system! ...
written 3 months ago by bruce.moran420
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Comment: C: MarkDuplicates RG ID on SAMRecord not found in header
... Thanks for the input. As soon as I posted I found the issue, as usual. I did have an @RG header, and it correct, but I used a tab-delimited variable via `RGLINE=$(echo -e "ID:XYZ\tPL:ILLUMINA")`, whereas STAR wants it as space-separated list. ValidateSamFile is happy with it anyway. ...
written 3 months ago by bruce.moran420
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MarkDuplicates RG ID on SAMRecord not found in header
... I am calling variants in RNAseq and exome data. Aligning with STAR, BWA MEM respectively. Get to MarkDuplicates and STAR BAMs give: Ignoring SAM validation error: ERROR: Record 1, Read name HWI-ST968:151:C1MMAACXX:1:1112:9825:81904, RG ID on SAMRecord not found in header: XYZ PL:ILLUMINA S ...
exome software error rna-seq written 3 months ago by bruce.moran420
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Comment: C: Can genomicranges do bedtools-like intersection operations?
... Great, just submitted an answer to your query ...
written 7 months ago by bruce.moran420
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Comment: A: Can genomicranges do bedtools-like intersection operations?
... Yes, it is possible. ...
written 7 months ago by bruce.moran420
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Comment: C: Can genomicranges do bedtools-like intersection operations?
... Try `findOverlaps`. You can then use `GenomicRanges::reduce` on a 'combined' GRanges object made from the combined set of reads (using `c()` works for that IIRC). With the option `revmap=TRUE`, you can backtrack to find which rows of the combined GRanges correspond to that region, and so that partic ...
written 7 months ago by bruce.moran420
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Answer: A: Sleuth PCA plots - how to change axis to percentage?
... I had the same question, so for anyone else coming across this: ppv <- plot_pc_variance(so) PCpc <- ppv$data$var names(PCpc) <- paste0("PC", seq(1:length(PCpc))) Also NB from [here][1] that TPM is probably not a good input to PCA. [1]: https://groups.google.com/forum/#!top ...
written 7 months ago by bruce.moran420
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Answer: A: duplicate 'row.names' are not allowed
... R will not allow you to have rownames that are the same for each row. Using a rowname in the first place is unnecessary. There is, IMHO, a better convention for data handling in R. Install the '[tidyverse][1]', load the library, read the count data into a [tibble][2]. The R 'base' offers a lot, but ...
written 7 months ago by bruce.moran420

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Popular Question 3 months ago, created a question with more than 1,000 views. For bedtools intersect -c flag output
Popular Question 10 months ago, created a question with more than 1,000 views. For bedtools intersect -c flag output
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Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Plot heatmap using pheatmap library
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