Moderator: dariober

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dariober11k
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Posts by dariober

<prev • 878 results • page 1 of 88 • next >
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Answer: A: snakemake different multiple input paths not in output or rule all
... If I understand correctly, I would make `path_to_bams.txt` a table that links input files to sample names, like this: sample infile s1 path/to/a.bam s2 path/to/b.bam s3 path/to/c.bam Then read this file in a pandas dataframe and use a lambda function to assign t ...
written 7 days ago by dariober11k
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Comment: C: How to avoid multiple mapped while no mismatch allow
... Can you provide an example of alignments you want to keep and examples that you want to filter out? ...
written 17 days ago by dariober11k
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Answer: A: Call alternative base for each position in a bam file
... See also this thread https://www.biostars.org/p/95700/ I suggested there [pysamstats](https://github.com/alimanfoo/pysamstats) and I'm still quite happy with it. ...
written 18 days ago by dariober11k
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Answer: A: How to avoid multiple mapped while no mismatch allow
... > What can i do to avoid reads that can find multiple perfectly matches If by that you mean to filter out reads that map equally well to multiple locations, then you should filter by MAPQ score in the alignment file, e.g. `samtools view -b -q 5 in.bam > out.bam`. The exact MAPQ threshold you ...
written 18 days ago by dariober11k
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Comment: C: Using R Studio on Cloud
... > Why don't you connect to the HPC with X11-forwarding and then run RStudio on the HPC? That could work but in my experience the X11-forwarding is painfully slow (that's why I wrote this [genome browser](https://asciigenome.readthedocs.io/en/latest/)). I use R a LOT and virtually all of it on re ...
written 6 weeks ago by dariober11k
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Answer: A: Whole-Exome Analysis on a Mainstream Desktop PC
... I agree that, depending on volume of data and turnaround time, doing NGS analysis on a desktop is possible these days. However, I find your comparison with HPC a bit misleading as I'm not sure that a single server with 40 CPUs can be considered a "high performance cluster" (by the way, what does C s ...
written 6 weeks ago by dariober11k
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Answer: A: UpsetR - How to display all possible intersections? How to change margins of ups
... To fix the issue with margins I think you have to play with the `attribute.plots` parameter and `theme(plot.margin = unit(c(...), "cm")))` (see examples in `?upset`). I think @Papyrus is correct about `nintersects` (+1, why not making it an answer?) ...
written 7 weeks ago by dariober11k
2
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Answer: A: I can/t use mkdir -p ~/bin
... Here's my guess (I don't have a MacOS to test). There is already a file `/Users/apple/bin` (a file, not a directory) so when you try to make a directory called `bin` in `/Users/apple` mkdir fails even if you have `-p` because you can't replace the file with a directory. I don't know why the comments ...
written 7 weeks ago by dariober11k
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Comment: C: Centrimo error: Template does not contain data section
... Thanks for this. `conda install 'meme=5.0.2' 'icu=58.2'` may be more explicit than `conda install bioconda/label/cf201901 meme` ...
written 7 weeks ago by dariober11k
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Comment: C: Hisat2 error: --read-lengths arg must be at least 20
... I also got this error with hisat2 v2.2.0 but v2.1.0 works fine. Must be a recent change...? ...
written 8 weeks ago by dariober11k

Latest awards to dariober

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

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