User: khorms
khorms • 150
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Posts by khorms
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... 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
khorms • 150
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... 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
khorms • 150
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... 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
khorms • 150
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Comment:
C: FeatureCounts with scRNA-seq
... Can you add a link to this article? ...
written 8 days ago by
khorms • 150
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... 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?
[ ...
written 9 days ago by
khorms • 150
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... 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
khorms • 150
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... 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
khorms • 150
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... 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
khorms • 150
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... 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
khorms • 150
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... 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
khorms • 150
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