Moderator: geek_y
geek_y ♦ 9.8k
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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
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... 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_y ♦ 9.8k
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Comment:
C: Allele specific expression
... How did you get that VCF file ? Genotyping array ? ...
written 22 days ago by
geek_y ♦ 9.8k
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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_y ♦ 9.8k
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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_y ♦ 9.8k
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... 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_y ♦ 9.8k
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... 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_y ♦ 9.8k
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... The chip-seq data is usually represented as peaks of genomic coordinates in bed file format. ...
written 8 weeks ago by
geek_y ♦ 9.8k
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154
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... > 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_y ♦ 9.8k
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... 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_y ♦ 9.8k
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... 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_y ♦ 9.8k
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