Moderator: geek_y
geek_y ♦ 8.8k
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I work with range of genomic data like transcriptome (RNA-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 genetics (eQTLs, caQTLs, hQTLs etc) to understand role of common genetic variants in genome regulation.
Posts by geek_y
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... why dont you use full path to run the program ? ...
written 17 hours ago by
geek_y ♦ 8.8k
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... Usually, its very hard to decide which gene it influence. It could influence Gene C which may be farther away than Gene A or Gene B. Best bet would be, check if both genes are expressed in the cell-type of your interest (if one of them is not expressed, you could eliminate that) , check if both gene ...
written 17 hours ago by
geek_y ♦ 8.8k
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... "amplicon sequence variants " - you mean the common and different variants between two datasets ? Does your organism has reference genome available ? ...
written 6 days ago by
geek_y ♦ 8.8k
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... Its a bit hard to follow but can you let me know your goal with RNA and ATAC ? and the genome build you are interested in ? ...
written 6 days ago by
geek_y ♦ 8.8k
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... Just convert your BED file to SAF and use [FeatureCounts][1] to quantify your BAM file over the features of your interest. Make sure your "BED" regions are not repeats or blacklisted on ucsc browser.
If you dont have coordinates of "unannotated" region, bin the genome into "n"KB bins and quantify y ...
written 6 days ago by
geek_y ♦ 8.8k
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... DHS is still open-chromatin region, so it can be a CTCF binding site or an inactive open-chromatin region. For an enhancer, it should have enhancer mark like H3K27Ac+H3K4Me1 or a bidirectional CAGE tags etc. ...
written 9 days ago by
geek_y ♦ 8.8k
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... You can do enrichment for overlaps using [LOLA][1]
To know the target genes of enhancers, you need to check if there is Hi-C "like" data for lungs. Otherwise, its pretty hard. The best is to assume the nearest "expressed" gene in lungs is the target.
[1]: https://academic.oup.com/bioinformatics ...
written 10 days ago by
geek_y ♦ 8.8k
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... If something is far promoter, its not necessarily an enhancer. ...
written 10 days ago by
geek_y ♦ 8.8k
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... Quantify the genes from both technical replicates and check the correlation between two samples. PCA might not give a good idea between technical replicates. Its good for biological replicates, as it takes only top 500 or 1000 genes. "Bad quality samples" either mean the initial RNA is of poor quali ...
written 3 months ago by
geek_y ♦ 8.8k
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... It depends. You could simply start with QTLtools or MatrixQTL which are easy fast to run. You could also go to more robust pipelines like RASQUAL which also models for allelic counts. ...
written 5 months ago by
geek_y ♦ 8.8k
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