User: khorms

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khorms210
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Moscow
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7 years, 7 months ago
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Posts by khorms

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Answer: A: Peak length for TF motif discovery
... I don't think there is a standard protocol for this, try different lengths. Regarding the background: if you do shuffling, make sure to keep the dinucleotide content (it's a very important predictor for many biological features). If you choose random positions from the genome, pick the ones where (1 ...
written 3 months ago by khorms210
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Comment: C: PhD in Bioinformatics: to continue, or not to continue? That is the question--
... Oh nice, good to hear that! ...
written 3 months ago by khorms210
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Comment: C: PhD in Bioinformatics: to continue, or not to continue? That is the question--
... I wonder what happened in the end? What did you choose? ...
written 3 months ago by khorms210
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Answer: A: Counting intronic or exonic reads for all genes
... I think there are plenty of tools that do this whole thing automatically for you; for example, see [CRIES][1] [1]: https://github.com/csglab/CRIES ...
written 4 months ago by khorms210
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Comment: C: Gene set enrichment analysis from ChIP-seq data
... I see; of the top of my head, I don't know any gene enrichment analysis tools that take replicates into account. Maybe you could use something like StereoGene ([link][1]) directly on your peaks? Now, if you want to do the search on gene level: in our lab, we use our own tool called iPAGE because it ...
written 4 months ago by khorms210
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Comment: C: Gene set enrichment analysis from ChIP-seq data
... Can you elaborate on what are you trying to accomplish? Do you have a list of peaks thresholded (peak / not a peak), or do you have a list of peaks ranked with p-values with no threshold? What kinds of pathways are you looking for: regulons, GO pathways, genome-wide correlations, etc? ...
written 4 months ago by khorms210
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Answer: A: Multi-group DE scRNA-seq comps without replicates
... Yes there are definitely methods for DE comparisons implemented in the commonly used single cell packages; for example, see this discussion ([link][1]) for scanpy [1]: https://github.com/theislab/scanpy/issues/397 ...
written 4 months ago by khorms210
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Answer: A: There are any good tutorial or book to help to get some stats in kmer analysis?
... When you are looking for overrepresented k-mers in biological sequences, you are usually comparing one group of sequences to another. That means that the background distribution has to come from the control group of sequences. I am not sure how are you planning to incorporate such background distrib ...
written 4 months ago by khorms210
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Comment: C: FeatureCounts with scRNA-seq
... Can you add a link to this article? ...
written 4 months ago by khorms210
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Standard format for SHAPE RNA reactivity data
... Is there a standard format for SHAPE RNA reactivity data? I am struggling to find one Looks like RNAstructure uses a two-column [format][1], ViennaRNA documentation doesn't talk about it too much [link][2]. It looks like every RNA lab does their own thing, is that so or am I missing something? [ ...
shape rna written 4 months ago by khorms210

Latest awards to khorms

Scholar 3 months ago, created an answer that has been accepted. For A: How to generate a mouse reference genome in STAR?
Scholar 8 months ago, created an answer that has been accepted. For A: How to generate a mouse reference genome in STAR?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Getting upstream of a given gene from a .gbk file
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Downloading genes annotations from UCSC Table Browser
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Visualisation of clusters produced by mothur
Popular Question 3.5 years ago, created a question with more than 1,000 views. For How to get the abundance of genes in metagenomes from MG RAST
Popular Question 4.0 years ago, created a question with more than 1,000 views. For How to get the abundance of genes in metagenomes from MG RAST
Popular Question 4.9 years ago, created a question with more than 1,000 views. For getting data from american gut project
Popular Question 6.1 years ago, created a question with more than 1,000 views. For How to get the abundance of genes in metagenomes from MG RAST

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