Moderator: geek_y
geek_y ♦ 11k
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Regulatory genomics and human genetics.
Posts by geek_y
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... By examining the intronic reads, you are evaluating if there is any unannotated coding exon that might be deferentially expressed. Or if you quantify intron retention events, you are evaluating alternative splicing differences. Both are biologically interesting, but it will be a lot of work. ...
written 5 days ago by
geek_y ♦ 11k
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... Probably those intronic reads are coming from unannotated exon or via an intron retention event. Did you check the bam file how the data looks and which introns ? You could simply get the intron coordinates ([leafcutter][1]) and identify introns from which those reads are coming from ([featurecounts ...
written 5 days ago by
geek_y ♦ 11k
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Comment:
C: Integrate four scRNA-seq datas
... Thats not a QC, that's normalization.
> for (i in 1:length(pancreas.list)) {
>
> pancreas.list[[i]] <- **NormalizeData**(pancreas.list[[i]], verbose =
> FALSE)
>
> pancreas.list[[i]] <- FindVariableFeatures(pancreas.list[[i]],
> selection.method = "vst", nfeatures = 2 ...
written 5 months ago by
geek_y ♦ 11k
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... why not using a simple samtools, awk ? Like `samtools view in.sorted.bam | awk '{ if ($5<255) print }' | cut -f3,4` ...
written 5 months ago by
geek_y ♦ 11k
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... amazing, as usual. ...
written 5 months ago by
geek_y ♦ 11k
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... Thanks. Very intuitive. ...
written 5 months ago by
geek_y ♦ 11k
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... may be you can create sliding windows and count SNPs within them and keep the ones that has more than 'n' SNPs. and then merge overlapping windows post-hoc to have a consensus loci. This can be achieved by bedtools and a bit of scripting. I am not aware of any tools that does this. ...
written 5 months ago by
geek_y ♦ 11k
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... If you are merging two seurat objects by `merge` function from Seurat, the resulting object is a Seurat object. So you dont need to create one. I am not sure what you are trying to do. The link you attached is about data integration and here you are merging. ...
written 6 months ago by
geek_y ♦ 11k
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For A: Breaking down the reference genome chromosome-wise
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For A: the analysis of multiple samples of 10X scRNA-seq
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For bedtools intersect: keep pairing consistent
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For Multiple sequence alignment between multi fasta files ?
Scholar
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For A: Breaking down the reference genome chromosome-wise
Scholar
5 months ago,
created an answer that has been accepted.
For A: Breaking down the reference genome chromosome-wise
Scholar
6 months ago,
created an answer that has been accepted.
For A: Breaking down the reference genome chromosome-wise
Scholar
6 months ago,
created an answer that has been accepted.
For A: Breaking down the reference genome chromosome-wise
Appreciated
6 months ago,
created a post with more than 5 votes.
For A: Biostars 3.0 under development. Visitor location is now displayed with a widget.
Great Question
6 months ago,
created a question with more than 5,000 views.
For Multiple sequence alignment between multi fasta files ?
Scholar
6 months ago,
created an answer that has been accepted.
For A: Breaking down the reference genome chromosome-wise
Popular Question
7 months ago,
created a question with more than 1,000 views.
For bedtools intersect: keep pairing consistent
Good Question
7 months ago,
asked a question that was upvoted at least 5 times.
For Convertion Of Gff3 To Gtf
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created an answer that has been accepted.
For A: Breaking down the reference genome chromosome-wise
Scholar
9 months ago,
created an answer that has been accepted.
For A: Breaking down the reference genome chromosome-wise
Scholar
9 months ago,
created an answer that has been accepted.
For A: Breaking down the reference genome chromosome-wise
Scholar
9 months ago,
created an answer that has been accepted.
For A: Breaking down the reference genome chromosome-wise
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