Moderator: geek_y

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geek_y9.8k
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I work with range of genomics data like transcriptome (RNA-Seq, scRNA-Seq, CAGE-Seq), open-chromatin/histone modifications/TF profiles, chromosome contact maps etc to understand tissue specific transcriptional regulation in human genome.

I also work on small part of genetics (eQTLs, caQTLs, hQTLs etc) to understand role of common genetic variants in genome regulation.

Posts by geek_y

<prev • 1,412 results • page 1 of 142 • next >
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Answer: A: Interpreting splice junctions on IGV
... I GUESS its showing splice junctions by strandedness of your reads. Thats why it looks symmetric. It doesn't matter if your gene goes left to right or right to left. ...
written 21 days ago by geek_y9.8k
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Comment: C: Allele specific expression
... How did you get that VCF file ? Genotyping array ? ...
written 22 days ago by geek_y9.8k
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Answer: A: Allele specific expression
... Thats the deviation from the expected 0.5. If you have 100 reads overlapping a het SNP, if 25 coming from ref and 75 coming from alt, Allelic Ratio (AR) **w.r.t ref** allele is `ref/total` `25/100 = 0.25` . So the deviation is `0.5-0.25=0.25` If there is no allelic imbalance, the ref reads would ...
written 24 days ago by geek_y9.8k
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Answer: A: Averaging multiple columns
... import pandas as pd df = pd.read_csv("tmp.txt", sep="\t", header=None) df 0 1 2 3 4 0 A 1 1 1 1 1 A 1 3 1 1 2 A 1 1 2 3 3 B 5 7 2 4 4 C 2 1 5 1 5 C 2 2 3 6 df.groupby(0).mean() 1 2 3 4 0 A 1.0 1.666667 1.333333 1.666667 B 5.0 7.00000 ...
written 24 days ago by geek_y9.8k
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Comment: C: de novo assembly of raw illumina reads of RNA seq experiment (24gb data)
... All the commercial software have a dedicated technical support. It would be useful to contact them as most of the people here use open-source tools. ...
written 7 weeks ago by geek_y9.8k
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Comment: C: How to validate the association between a ranked list of genes found computation
... If you have list of genes associated with disease, you could do [GSEA][1]. [1]: http://software.broadinstitute.org/gsea/index.jsp ...
written 7 weeks ago by geek_y9.8k
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Comment: C: what does the bed file in bedtools multicov command refer to ?
... The chip-seq data is usually represented as peaks of genomic coordinates in bed file format. ...
written 8 weeks ago by geek_y9.8k
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Comment: C: what does the bed file in bedtools multicov command refer to ?
... > I want to use multicov mode to get **reads count on my chip seq reads** Where do you want to measure the read counts ? ...
written 8 weeks ago by geek_y9.8k
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Answer: A: Single cell-seq data preprocessing-How to detect the gene/transcript distributio
... 2000 genes could be the most variable genes across cells which will be used for PCA and then t-SNE/UMAP. Filtering cells should be defined in methods of the paper. Abnormally high UMI counts, high mitochondrial genes, low number of genes captured, low sequencing depths, doublets etc can be some of ...
written 8 weeks ago by geek_y9.8k
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Answer: A: The distance in nucleotide between two genes on different strands
... To me, distance between two genes would be the distance between the two transcriptional start sites. So I would just take the two TSS and get the absolute differences between them. This makes sense if you are looking into transcriptional regulation as its about promoters ( even if its about enhancer ...
written 8 weeks ago by geek_y9.8k

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