Moderator: dariober
dariober ♦ 11k
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Posts by dariober
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Comment:
C: BWA mem minimum read length
... Have you checked whether the 35 bp reads are all Ns? bcl2fastq, the program most commonly used to generate fastq files from raw bcl, by default resets reads too short after adtapter trimming to a strech of 35 Ns. This could explain the 35 to 36 bp gap. ...
written 2 hours ago by
dariober ♦ 11k
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... Try downloading the tar.gz file to your machine then do `install.packages('inSilicoDb_1.10.1.tar.gz', repos= NULL)` ...
written 3 days ago by
dariober ♦ 11k
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... It appears write_xlsx doesn't have a parameter `row.names`. Why don't you just add a column for row names to the dataframe `dd` before writing it? Like:
dd$row_names <- rownames(dd)
dd <- dd[, c(ncol(dd), 1:(ncol(dd)-1))] # Make row_names first column ...
written 3 days ago by
dariober ♦ 11k
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... I can't tell for sure what's going on but you may need to install some additional packages like Biobase, rjson, RCurl (in my sessionInfo, check the list under `other attached packages:` and `loaded via a namespace`) ...
written 3 days ago by
dariober ♦ 11k
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... Odd... Can you post the output of `sessionInfo()`? This works for me on R3.6:
install.packages('https://www.bioconductor.org/packages/2.13/bioc/src/contrib/inSilicoDb_1.10.1.tar.gz')
inferring 'repos = NULL' from 'pkgs'
trying URL 'https://www.bioconductor.org/packages/2.13/bioc/src/con ...
written 4 days ago by
dariober ♦ 11k
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... Looking at [this](https://cran.r-project.org/bin/windows/Rtools/), it seems that Rtools for R 4.0 is actually `Rtools40`. Try following instructions there.
I don't mean to sound discouraging but you are a bit in a tricky situation because 1) You are using Windows (most bioinformatics tools are des ...
written 4 days ago by
dariober ♦ 11k
1
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... I think you can install from source like this using your required versions:
install.packages('https://www.bioconductor.org/packages/2.13/bioc/src/contrib/inSilicoDb_1.10.1.tar.gz')
install.packages('https://www.bioconductor.org/packages/2.13/bioc/src/contrib/inSilicoMerging_1.6.0.tar.gz')
...
written 4 days ago by
dariober ♦ 11k
1
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3
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Answer:
A: update salmon with conda
... `PackagesNotFoundError`: Do you have the bioconda channel available? You can check with:
conda config --show channels
Which should print something like:
channels:
- conda-forge
- bioconda
- defaults
If you don't see bioconda there, check the [installation instructions]( ...
written 9 days ago by
dariober ♦ 11k
0
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... As I say in my answer, the defaults for mapping quality are different and featureCounts does not filter for mapping quality by default. Since you mention transposones, it may well be that you have lots of reads with MAPQ 0 hence more counts with featureCounts. ...
written 10 days ago by
dariober ♦ 11k
0
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1
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86
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... Can you post the commands you used for both featureCounts and htseq and the summary statistics they produce?
For one thing, the two programs have different defaults for filtering reads on mapping quality.
featureCounts v1.6.4:
-Q The minimum mapping quality score a read must sat ...
written 11 days ago by
dariober ♦ 11k
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For A: Visualize reads in BAM file
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For C: Adapter trimming tool for Windows?
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For A: Replace fields CHROM and POS in a vcf file
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