Moderator: Goutham Atla

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Goutham Atla7.0k
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Computational Biology. Marie-Curie ESR. Regulatory genomics. Beta-cell biology. 

Posts by Goutham Atla

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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 3 days ago by Goutham Atla7.0k
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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 3 days ago by Goutham Atla7.0k
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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 5 days ago by Goutham Atla7.0k
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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 8 days ago by Goutham Atla7.0k
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Comment: C: BioStar's List of Predatory Journals and Publishers to Avoid - Spring Cleaning 2
... The guy involved in recopublishers or biscuitglobal is a very dodgy person on social media, uses many false credentials. I have been keeping an eye on him. ...
written 14 days ago by Goutham Atla7.0k
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Answer: A: Benchmark papers for Chip genomic enrichment
... https://omictools.com/peak-calling-category Not all listed are peak calling softwares, but it covered most of the notable ones. ...
written 23 days ago by Goutham Atla7.0k
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Answer: A: A possible script request for a task probably cannot be done in Excel
... Assuming the tab delimited file: sort -k1,1 in.txt | groupBy -g 1 -c 2 -o mean > out.txt `out.txt`: A2M -11.045 ACE 1.68 ACYP2 7.16 ADAMTS12 1.71 ADAMTS6 5.36 ADIPOQ 2.885 AGR2 4.785 [groupBy][1] from bedtools [1]: http://bedtools.readthedocs.io/en/latest/c ...
written 23 days ago by Goutham Atla7.0k
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Comment: C: How To Get A List Of All Correlated Snps (In Ld) With Another List Of Snps?
... Were you able to resolve this ? ...
written 26 days ago by Goutham Atla7.0k
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Comment: C: Determine promoter regions relative to TSS.
... What kind of data it is ? TFs ? Histone modification ? Looks like you are trying to find the direct targets of a TF. Generally +/- 500bp from TSS is considered as promoter. If you go beyond like 2kb or 5kb, they would be distal regulatory elements, not direct targets. ...
written 27 days ago by Goutham Atla7.0k
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Comment: C: 3' UTR sequence
... You need to convert your fasta header of CDS to a bed format. ...
written 6 weeks ago by Goutham Atla7.0k

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Popular Question 4 days ago, created a question with more than 1,000 views. For Annotation Bed File For Phaseolus Vulgaris
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Scholar 8 days ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Teacher 23 days ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Confusion In Pdb File Format
Scholar 6 weeks ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
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Popular Question 7 weeks ago, created a question with more than 1,000 views. For Confusion In Pdb File Format
Scholar 9 weeks ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Confusion In Pdb File Format
Scholar 11 weeks ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
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Scholar 3 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
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Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: htseq-count for RNA Seq
Popular Question 4 months ago, created a question with more than 1,000 views. For comparing vcf files of disease and normal samples
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