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Answer: Sub-sampling a BAM to a fixed number of reads
Comment: Downsample BAM file to specific amount of reads
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
Answer: genome finishing
Comment: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
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Recent Replies
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 because you are running the ARM based conda. Bioinformatics software is compiled for Intel based CPUs only. Uninstall that …
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…
Comment: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
by
Pierre Lindenbaum
161k
> I haven't been able to figure out how to generate this plot. show us what you tried and the error messages
Comment: Duplicated reads (IDs) from nanopore sequencing
by
njornet
▴ 20
I think this is the answer but I can't find in the tags info about primary and secondary alignments. I've only found in the flag that the s…
Answer: Add stats to boxplot in R
by
Lélé
• 0
Hi, Have you tried switching the order of the stat_compare_means for the Wilcox with the one for kruskall-Wallis ?
Comment: genome finishing
by
Joe
21k
I may be wrong here so someone feel free to correct me, but I've never noticed a variants file from `SPAdes`, and certainly never used one …
Comment: perseus software (version 1.5.5)
by
Joe
21k
You will need to obtain the software from an official source. I believe Perseus is a paid-for program and as such sharing via the forum wou…
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