Moderator: geek_y

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geek_y8.8k
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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

<prev • 1,328 results • page 1 of 133 • next >
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Comment: C: how to use tool installed in local directory to work in script to submit job on
... why dont you use full path to run the program ? ...
written 17 hours ago by geek_y8.8k
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Answer: A: ChIP-Seq annotation question: Should gene annotation based on the nearest TSS or
... 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_y8.8k
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Comment: C: Identifying shared exact sequence variants between two datasets
... "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_y8.8k
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Comment: C: Aligning RNA-seq and ATAC-seq gene annotations
... 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_y8.8k
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Answer: A: How to extract un annotated (With abundant) small RNA transcript?
... 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_y8.8k
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Comment: C: How to find out whether Chip-seq peaks falls within promoter or enhancer region
... 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_y8.8k
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Comment: C: How to find out whether Chip-seq peaks falls within promoter or enhancer region
... 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_y8.8k
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Comment: C: How to find out whether Chip-seq peaks falls within promoter or enhancer region
... If something is far promoter, its not necessarily an enhancer. ...
written 10 days ago by geek_y8.8k
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Answer: A: Sequenced sample twice, can I merge the fastqs to analyze?
... 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_y8.8k
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Comment: C: How to approach QTL for transcriptomic data?
... 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_y8.8k

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