Moderator: geek_y

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geek_y8.0k
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Computational Biology. Marie-Curie ESR.

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 the transcriptional regulation as a whole.

 

Posts by geek_y

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Comment: C: How to obtain RPKM/FPKM from HTSeq-Count data?
... I assumed that you already have the RPKM from this **"Could I just download the RPKM files of miRNAs and genes from GDC data portal"** I would suggest to speak to someone in your workplace who does bioinformatics. If you are starting with RNA-Seq analysis and wants to work with TCGA, it needs lot ...
written 3 days ago by geek_y8.0k
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Answer: A: How to obtain RPKM/FPKM from HTSeq-Count data?
... There is no much use of calculating RPKM/FPKM for miRNAs. To answer your question, you can use [featureCounts][1] to quantify your genes using a GTF file. This outputs a matrix of counts, which also includes a column of gene lengths. This column can be given to edgeR `rpkm()` function. Option 3 w ...
written 3 days ago by geek_y8.0k
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Comment: C: next step after differential expression analysis
... I would definitely encourage people to search google or biostars posts when ever possible. ...
written 3 days ago by geek_y8.0k
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Answer: A: next step after differential expression analysis
... You can use [Enrichr][1] on up and down regulated genes separately to find enriched GO terms or pathways and many more gene sets. To visualise, to make it simple, I would just plot a heat map of differential genes and highlight important gene names, enriched in GO or pathway analysis. You can also ...
written 3 days ago by geek_y8.0k
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Comment: C: Peak calling macs vs Homer
... I also spent lot of time on MACS2 to analyse around 100 in-house generated chromatin data sets including ATAC-Seq, several TFs and several histone modifications. I agree that there are some discrepancies on statistics employed by MACS2, the way it defines significant peaks, but there are well accept ...
written 6 days ago by geek_y8.0k
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Comment: C: Which mapping tool takes read quality score into account
... Thats why we filter the data before aligning. SNP callers can distinguish sequencing errors from real SNPs ...
written 7 days ago by geek_y8.0k
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Comment: C: TAD (Topologically Associating Domain) boundaries
... Your question is about TADs and now you are looking at GRB. Both are different. ...
written 10 days ago by geek_y8.0k
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Comment: C: TAD (Topologically Associating Domain) boundaries
... Which genome ? ...
written 10 days ago by geek_y8.0k
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Comment: C: How to generate FPKM value for each replicates?
... Though cuffdiff is for differential expression, it generates the FPKM/RPKM values ...
written 23 days ago by geek_y8.0k
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Answer: A: How to generate FPKM value for each replicates?
... If you inspect all the files, there will files with rpkm for each replicate. **From [cuffdiff][1] website:** > Cuffdiff calculates the expression and fragment count for each > transcript, primary transcript, and gene in each replicate. The > results are output in per-replicate tracking f ...
written 23 days ago by geek_y8.0k

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