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Bioawk - Fasta, Fastq, Sam, Bed, Gff Aware Awk Programming
Bioawk - Fasta, Fastq, Sam, Bed, Gff Aware Awk Programming
A: extract dendrogram cluster from pheatmap
A: extract dendrogram cluster from pheatmap
A: Why Does Rna-Seq Read Count Fit Poisson Distribution?
A: Why Does Rna-Seq Read Count Fit Poisson Distribution?
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Comment: quick way to get samples that are NOT homozygous reference for a given record us
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curious
▴ 500
`[filter.c:1379 filters_init1] Error: the tag "INFO/count" is not defined in the VCF header` ?
Comment: Bioinformatics definition of TAD boundary
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kalavattam
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> Can anyone provide a formal definition of TAD boundaries in bioinformatic language? There's not a consensus definition of TAD boundaries…
Comment: Transcript enrichment in Illumina RNAseq
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compuTE
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Thank you @friederike I'll check it out!
Comment: Bam file metrics
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Ram
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Is it (samtools stat) fast though? I recall samtools being really slow compared to sambamba.
Answer: Bam file metrics
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heskett
▴ 10
Samtools stats is a new option for this. samtools is very reliable and easy to use in my experience
Comment: Single cell RNA-seq: how many PCs to use for t-SNE/UMAP?
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MutationalMeltdown
▴ 130
It depends, checks are essential but it can become too subjective if you're tweaking parameters to find 'what you want'- I also need standa…
Comment: ICE normalization using JuicerTools
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kalavattam
▴ 50
I might be mistaken, but I think 'bias' and 'weight' are synonyms in cooler/cooltools, e.g., [link][1] [1]: https://github.com/open2c/c…
Comment: Single cell RNA-seq: how many PCs to use for t-SNE/UMAP?
by
MutationalMeltdown
▴ 130
Thanks, I have used autocoders this way (was introduced by [this tutorial][1]). However, I've never actually found an autoencoder viz that …
Comment: design matrix considering treatment, timepoints and batches
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Iván
▴ 50
Anyone willing to input on this? Thank you! :-)
Answer: How to extend ChIP-seq reads from BAM file ?
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heskett
▴ 10
Bedtools slop can add bases in both or either directions to a read. very easy to use
Comment: XGBoost on the unbalanced data
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Mensur Dlakic
★ 10k
> The task sounds like pretty balanced When one has 51:49 ratio of classes, or 55:45, or even 60:40, we can call that pretty balanced. A 1…
Answer: quick way to get samples that are NOT homozygous reference for a given record us
by
Pierre Lindenbaum
135k
bcftools view -i 'count(GT=="RR")==0'
Comment: How to combine 2 incomplete GTF
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Juke34
★ 5.4k
Could you show few lines of the original file? You will probably need to create proper gene feature first using an appropriate attribute (u…
Comment: Single cell RNA-seq: how many PCs to use for t-SNE/UMAP?
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Mensur Dlakic
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I am not necessarily recommending autoencoders for visualization over t-SNE/UMAP either. In fact, I said above `it may not work for all dat…
Answer: Whole genome species clustering
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h.mon
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I don't think there is a "best" approach in your situation, given 1) the taxonomy of the group is probably still flaky. 2) being dra…
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