Moderator: geek_y

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geek_y9.3k
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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 • 1,371 results • page 1 of 138 • next >
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Comment: C: % of change and log2 fold change (L2FC)?
... If you do `2^log2FC`, which tells how many folds the change is. Here `2^3.3=9.8` folds. The sign gives information about the up/down regulation. ...
written 6 hours ago by geek_y9.3k
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Answer: C: % of change and log2 fold change (L2FC)?
... seems correct to me. log2FC is more informative as you will see the direction (sign) and the effect. Treatment = 10 Control = 100 `FoldChange = 10/100 = 0.1` which is not informative `log2FC = log2(10)-log2(100) = -3.3` which tells the effect and direction. ...
written 17 hours ago by geek_y9.3k
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Comment: C: Insert size of -20bp with ATAC-seq?
... can you post the plot of "distribution of insert size" ? Its common to observe a sharp peak less than 100bp but you should also see a peak of 150-200bp and then around 300bp. ...
written 17 hours ago by geek_y9.3k
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Comment: C: how to perform interaction and binding site between lncRNA and mRNA?
... There is a correlation at gene expression levels/transcription between mRNA and it's putative lncRNA but other than that, there are several mechanisms about lncRNA function. I did not understand "binding" part. Do you mean the lncRNA binding to it's target mRNA ? ...
written 1 day ago by geek_y9.3k
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Comment: C: Differences between motif enrichment analysis and footprinting in the context of
... I added a link to review ...
written 3 days ago by geek_y9.3k
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Answer: A: Differences between motif enrichment analysis and footprinting in the context of
... Motif enrichment analysis is checking if there are any over represented sequences through PWMs in the regions/peaks of your interest. Foot-printing based on deep sequenced ATAC/DNAse data tells you if something is really bound to peaks of interest. If you imagine a transcription factor is boun ...
written 3 days ago by geek_y9.3k
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Answer: A: Mapping to transcriptome with bowtie2 vs mapping to genome using STAR
... figured it out. Sometimes annotations includes 3' UTRs. So if the annotations we are using includes 3' UTRs, we get counts for genes. If not, we dont quantify them. Its not problem of mapping but the annotations we are using. ![enter image description here][1] [1]: https://i.ibb.co/9YPFCnV/Scr ...
written 5 days ago by geek_y9.3k
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Comment: C: Mapping to transcriptome with bowtie2 vs mapping to genome using STAR
... I STAR re-aligned using very low stringent options, no luck so far. I am going to try exact method the authors described in their paper. ...
written 5 days ago by geek_y9.3k
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Mapping to transcriptome with bowtie2 vs mapping to genome using STAR
... Hi, Does any one know any paper or personally compared the results of the following approaches ? 1. Mapping RNA-Seq reads to transcriptome fasta using bowtie2 and quantifying using RSEM or other tools. 2. Mapping RNA-Seq data to genome fasta using STAR and quantifying using featureCounts. In fir ...
bowtie2 star rna-seq written 5 days ago by geek_y9.3k
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Comment: C: the peaks of ChIPseq are few
... Different peaks means gain or loss of peaks from A to D, which could be biologically true but you need to have replicates and perform a differential analysis like using DESeq2. ...
written 7 days ago by geek_y9.3k

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