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A: how to combine RNA seq data from 4 lanes
Answer: Cannot install bwa-mem2 via conda
Answer: Sub-sampling a BAM to a fixed number of reads
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Answer: Long reads and fixing of mate-pair issues/marking duplicates with samtools
Answer: Long reads and fixing of mate-pair issues/marking duplicates with samtools
Answer: genome finishing
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Recent Replies
Comment: Add stats to boxplot in R
by
Lélé
• 0
To remove "Kruskall Wallis" you can try adding the argument label="p" or label = "p.signif" which displays the p-value or *** like this: …
Answer: Sequencing Depth (Read Depth) Calculations
by
GenoMax
142k
You could also use `pandepth` ([**LINK**][1]) or `mosdepth` ([**LINK**][2]) as well. These will allow you to be flexible about windowed cov…
Comment: Sequencing Depth (Read Depth) Calculations
by
Pierre Lindenbaum
161k
it looks looks ok to me. <!-- This cmd works and gives me 40.5235, I was wondering whether this cmd is right or wrong, and does anyone hav…
Comment: Add stats to boxplot in R
by
Ghada
• 0
Great. thats work. Do you know how can I remove the kruskall-Wallis name from the plot? Also I would like to draw a line under the kruskall…
Comment: Using ggplotly in R
by
jared.andrews07
★ 16k
Again, this is not particularly difficult to do with [plotly itself](https://plotly.com/r/line-and-scatter/#adding-color-and-size-mapping) …
Comment: Duplicated reads (IDs) from nanopore sequencing
by
GenoMax
142k
If you only have supplementary alignments then they may be caused by reasons mentioned here --> https://www.biostars.org/p/308853/ I did no…
Comment: Cannot install bwa-mem2 via conda
by
Pierre Lindenbaum
161k
> Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the c…
Answer: Cannot install bwa-mem2 via conda
by
Istvan Albert
100k
The problem is caused by running the ARM-based conda. Bioinformatics software is compiled for Intel based CPUs only. Uninstall that versio…
Comment: Duplicated reads (IDs) from nanopore sequencing
by
marco.barr
▴ 110
[https://www.biostars.org/p/9559284/][1] you could try this [1]: https://www.biostars.org/p/9559284/
Comment: Duplicated reads (IDs) from nanopore sequencing
by
marco.barr
▴ 110
it's also true that now I only have one pod5 folder, thanks anyway for clarifying the focus of the issue. Yes, they are probably secondary …
Comment: Applying the metacell2 algorithm using python
by
Wayne
★ 2.0k
I'm unsure. I will say that looking for [ normalize](https://github.com/search?q=repo%3Atanaylab%2Fmetacells%20normalize&type=code) among t…
Comment: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
by
Pierre Lindenbaum
161k
> Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the c…
Answer: genome finishing
by
nd48
▴ 20
What is the input? Do you have short reads (e.g. illumina 100bp paired reads)? As mentioned already, you already have the consensus i.e. c…
Comment: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
by
biology_inform
▴ 50
I've been exploring different visualization tools like Circos and shinyCircos, and I've noticed that they require an input file similar to …
Answer: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
by
Papyrus
★ 2.9k
If you want to plot global accessibility, maybe you would like to plot the ATAC "signal", instead of specific peaks. In a very general mann…
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