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kalavattam
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JC
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Michael Dondrup
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MutationalMeltdown
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Recent Replies
Comment: quick way to get samples that are NOT homozygous reference for a given record us
by
Pierre Lindenbaum
135k
what is your version of bcftools ? check you're using a recent version.
Answer: How to analysis 4c seq 3c seq data
by
kalavattam
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50
To start, you can check [this paper][1], "4C-seq from beginning to end: A detailed protocol for sample preparation and data analysis," and …
Answer: recent Hi-C databases
by
kalavattam
▴
50
- Data, including 3C-related/derived data, for the 4DNucleome project are here: [https://data.4dnucleome.org/][1]
- All data for the ENC…
Comment: quick way to get samples that are NOT homozygous reference for a given record us
by
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
by
kalavattam
▴
50
> 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
by
compuTE
▴
60
Thank you @friederike I'll check it out!
Comment: Bam file metrics
by
Ram
32k
Is it (samtools stat) fast though? I recall samtools being really slow compared to sambamba.
Answer: Bam file metrics
by
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?
by
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
by
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/…
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
by
Iván
▴
50
Anyone willing to input on this? Thank you! :-)
Answer: How to extend ChIP-seq reads from BAM file ?
by
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
by
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'
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