Moderator: dariober

gravatar for dariober
dariober11k
Reputation:
11,190
Status:
Trusted
Location:
WCIP | Glasgow | UK
Website:
https://github.com/dar...
Last seen:
6 minutes ago
Joined:
8 years ago
Email:
d************@gmail.com

about me

Posts by dariober

<prev • 901 results • page 1 of 91 • next >
0
votes
0
answers
50
views
0
answers
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 dariober11k
1
vote
2
answers
118
views
2
answers
Comment: C: There is a convenient way to use not up-to-date packages in R?
... 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 dariober11k
2
votes
1
answer
46
views
1
answers
Answer: A: write.xlsx with row.names=TRUE giving error "unused argument (row.names=TRUE)
... 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 dariober11k
0
votes
2
answers
118
views
2
answers
Comment: C: There is a convenient way to use not up-to-date packages in R?
... 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 dariober11k
0
votes
2
answers
118
views
2
answers
Comment: C: There is a convenient way to use not up-to-date packages in R?
... 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 dariober11k
2
votes
2
answers
118
views
2
answers
Comment: C: There is a convenient way to use not up-to-date packages in R?
... 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 dariober11k
1
vote
2
answers
118
views
2
answers
Answer: A: There is a convenient way to use not up-to-date packages in R?
... 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 dariober11k
1
vote
3
answers
96
views
3
answers
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 dariober11k
0
votes
1
answer
86
views
1
answers
Comment: C: Difference in the counts generated using FeatureCounts and HTseq
... 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 dariober11k
0
votes
1
answer
86
views
1
answers
Answer: A: Difference in the counts generated using FeatureCounts and HTseq
... 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 dariober11k

Latest awards to dariober

Scholar 3 days ago, created an answer that has been accepted. For A: Visualize reads in BAM file
Scholar 12 days ago, created an answer that has been accepted. For A: Visualize reads in BAM file
Scholar 9 weeks ago, created an answer that has been accepted. For A: Visualize reads in BAM file
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Visualize reads in BAM file
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Visualize reads in BAM file
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: count the number of transcription factor binding sites
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Visualize reads in BAM file
Popular Question 4 months ago, created a question with more than 1,000 views. For Computational Biologist - Cambridge University/CRUK
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Visualize reads in BAM file
Scholar 5 months ago, created an answer that has been accepted. For A: Visualize reads in BAM file
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Visualize reads in BAM file
Appreciated 5 months ago, created a post with more than 5 votes. For A: Output the color code according to number
Scholar 7 months ago, created an answer that has been accepted. For A: Visualize reads in BAM file
Appreciated 7 months ago, created a post with more than 5 votes. For A: Output the color code according to number
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Visualize reads in BAM file
Scholar 7 months ago, created an answer that has been accepted. For A: Visualize reads in BAM file
Appreciated 8 months ago, created a post with more than 5 votes. For A: Output the color code according to number
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Visualize reads in BAM file
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Visualize reads in BAM file
Appreciated 10 months ago, created a post with more than 5 votes. For A: Output the color code according to number
Prophet 10 months ago, created a post with more than 20 followers. For ChIP-Seq: Calling peaks with replicates
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Adapter trimming tool for Windows?
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: count the number of transcription factor binding sites
Scholar 10 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1837 users visited in the last hour