Moderator: Goutham Atla

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Goutham Atla7.1k
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Computational Biology. Marie-Curie ESR. Regulatory genomics. Beta-cell biology. 

Posts by Goutham Atla

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Comment: C: Calling peaks with macs2 if not all replicates have a corresponding input-file
... Its need not be scaling treatment to control always. It scales the sample with large number of reads to sample with smaller number of reads. ...
written 21 hours ago by Goutham Atla7.1k
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Comment: C: Calling peaks with macs2 if not all replicates have a corresponding input-file
... I would pool all control samples and call peaks on each treatment sample independently. macs2 callpeak -t tfile1.bam -c ctrl_pooled.bam ...
written 21 hours ago by Goutham Atla7.1k
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Answer: A: Effects of some especial non-coding regions
... A quick thing to do is to upload them to [GREAT][1] Other long and complicated strategy is to check if those non-coding regions are a part of any regulatory elements. Data from Roadmap Epigenomics or ENCODE will give you the regulatory regions across multiple tissues. You can intersect your region ...
written 21 hours ago by Goutham Atla7.1k
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Answer: C: why dont we need technical replicate in case of RNA Seq.?
... I don't think "**RNA seq is new emerging technology**". You don't need technical replicates but you need biological replicates. For allele isoform expression, you need many samples ( as you need to work with genotypes ) with more sequencing depth than that is required for DGE. ...
written 21 hours ago by Goutham Atla7.1k
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Comment: C: Upstream Regulator Gene Differential expression
... How many replicates do you have ? What does the PCA tells ? Does it clearly separates the WT and KO ? Does the GO of these differential genes agree with the biological function of SOX2 ? Instead of looking for IPA etc, you can do a motif enrichment analysis ( Homer/FIMO etc ) on the promoters/proxim ...
written 1 day ago by Goutham Atla7.1k
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Answer: A: Can I run ENCODE ChIP-Seq pipeline or get their code?
... You can definitely run. All the scripts are on github with a detailed protocol. https://github.com/kundajelab/chipseq_pipeline ...
written 23 days ago by Goutham Atla7.1k
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Answer: A: CAGE seq & RNA-seq
... Most of the data from CAGE protocol comprised of only 5' end and usually short reads. So you can not use CAGE data to study fusion, unless you have a long read PE CAGE data. CAGE-Seq and RNA-Seq are complimentary to each other in terms of studying the gene expression levels, as long as you have dat ...
written 4 weeks ago by Goutham Atla7.1k
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Answer: C: Regulatory feature to gene annotation
... You can search literature that predicts the enhancer-promoter interactions.For example, you may find papers like [Enhancer–promoter interactions are encoded by complex genomic signatures on looping chromatin][1] [1]: http://www.nature.com/ng/journal/v48/n5/full/ng.3539.html ...
written 4 weeks ago by Goutham Atla7.1k
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Comment: C: Does MACS2 or MACS14 perform total reads normalization?
... The chip and control reads are scaled to same sequencing depth ( towards lower ) before doing a poisson test for signal enrichment. ...
written 4 weeks ago by Goutham Atla7.1k
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Answer: A: What does "gappedPeak" mean
... GappedPeak is a representation of narrow peaks as blocks over a broad peak. To trick the visualisation tools, they use the same format as gene models, but use the narrow peak coordinates as exons coordinates and the broad peak coordinates as coding region coordinate. ...
written 5 weeks ago by Goutham Atla7.1k

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