Moderator: geek_y

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geek_y11k
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Regulatory genomics and human genetics.

Posts by geek_y

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Comment: C: Tools to Study Intronic Regions from RNA-Seq Data
... 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_y11k
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Answer: A: Tools to Study Intronic Regions from RNA-Seq Data
... 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_y11k
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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_y11k
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Comment: C: RNA-seq STAR genome mapping
... Good catch. ...
written 5 months ago by geek_y11k
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Comment: C: How to find all mapped locations of a read from PySam?
... 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_y11k
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Comment: C: filtered tab delimited file with awk
... amazing, as usual. ...
written 5 months ago by geek_y11k
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Comment: C: differential gene expression analysis
... Thanks. Very intuitive. ...
written 5 months ago by geek_y11k
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Comment: C: differential gene expression analysis
... What is GSE ? ...
written 5 months ago by geek_y11k
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Comment: C: Keeping loci those have specific number of SNPS
... 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_y11k
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Comment: C: merge two SeuratObjects to do the integration
... 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_y11k

Latest awards to geek_y

Scholar 5 days ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: the analysis of multiple samples of 10X scRNA-seq
Popular Question 5 months ago, created a question with more than 1,000 views. For bedtools intersect: keep pairing consistent
Great Question 5 months ago, created a question with more than 5,000 views. For Multiple sequence alignment between multi fasta files ?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Scholar 5 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
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
Great Question 6 months ago, created a question with more than 5,000 views. For Multiple sequence alignment between multi fasta files ?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Scholar 6 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
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
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Scholar 8 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
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Scholar 9 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise

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