User: khorms

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khorms150
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Moscow
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7 years, 3 months ago
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Posts by khorms

<prev • 45 results • page 1 of 5 • next >
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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 2 days ago by khorms150
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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 2 days ago by khorms150
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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 7 days ago by khorms150
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Comment: C: FeatureCounts with scRNA-seq
... Can you add a link to this article? ...
written 8 days ago by khorms150
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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 9 days ago by khorms150
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Answer: A: Should I do normalization to gene/features or samples?
... Normalize columns (samples), not rows (features), because what you are aiming to find is the features with large changes between the sample groups, and you will kill the magnitude of changes if you normalize by features ...
written 3 months ago by khorms150
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Answer: A: Extracting features corresponding to low entropy regions from RNAfold output
... From RNAfold [documentation][1]: "It also produces PostScript files with plots of the resulting secondary structure graph and a "dot plot" of the base pairing matrix. The dot plot shows a matrix of squares with area proportional to the pairing probability in the upper right half, and one square for ...
written 3 months ago by khorms150
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Answer: A: Syntax for samtools flagstat on multiple .bam files outputting to .txt file
... An easy way of doing it is to run samtools flagstat on multiple .bam files and then combine their output together using [multiqc][1] So something like samtools_stat_commands=() samtools_stat_log_folder='' multiqc_folder='' for i in ${aligned_folder}/*.bam do sample_name=$(basename $ ...
written 4 months ago by khorms150
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Answer: A: Blood Derived Normal RNA_seq samples TCGA
... I don't think there are any. In order to double check, you could do this: This [table][1] show the codes for sample types; so all you need to know to figure out what kind of sample you are looking at is the last two digit barcode. You could go to [Xena][2], look at the pages corresponding to the ...
written 4 months ago by khorms150
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Answer: A: Test if a list of genes with coordinates are expressed (hisat2 data)
... You could use [IGV][1] to visualize both your alignment .bam file and your bed file; this way you could manually inspect the regions of interest [1]: http://software.broadinstitute.org/software/igv/ ...
written 4 months ago by khorms150

Latest awards to khorms

Scholar 4 months ago, created an answer that has been accepted. For A: How to generate a mouse reference genome in STAR?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Getting upstream of a given gene from a .gbk file
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Downloading genes annotations from UCSC Table Browser
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Visualisation of clusters produced by mothur
Popular Question 3.1 years ago, created a question with more than 1,000 views. For How to get the abundance of genes in metagenomes from MG RAST
Popular Question 3.7 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 4.6 years ago, created a question with more than 1,000 views. For getting data from american gut project
Popular Question 5.8 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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