User: dr_bantz

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dr_bantz50
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Posts by dr_bantz

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Compare SE sequence with PE sequnce?
... As I understand it, the OP is trying to compare expression in one set of samples done with SE with that of another set done with PE, so adding SE/PE as a covariate will make no difference. If that's not the case then yes, you're correct. ...
written 3 months ago by dr_bantz50
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Comment: C: Compare SE sequence with PE sequnce?
... Were the different sample sets from different labs or even from the same lab but taken at different times/conditions? If so, I would be extremely wary of batch effects, which often have a very strong influence over RNA-seq data. In terms of differences purely between 50 bp SE vs 100 bp PE, the latt ...
written 3 months ago by dr_bantz50
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Answer: A: Renaming Bedtools outputs individually
... Let's say your file has the following columns: 1. chromosome 2. start 3. end 4. name You read this into R as "data": data <- read.table("file.bed", sep = "\t", colnames = c("chromosome", "start", "end", "name") In R, it's pretty easy to rename based on position: data[data$chromosome ...
written 3 months ago by dr_bantz50
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Comment: C: snakemake input pattern
... SAMPLES = [] samp_lane = [] for samp,lane in config["samples"].items(): SAMPLES.append(samp) samp_lane = lane I'm guessing that should be samp_lane.append(samp) in the for loop? Either way, the wildcards probably won't work as you expect them to. It might be considerabl ...
written 5 months ago by dr_bantz50
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Pairwise alignment sliding window across the whole genome
... There is a hexanucleotide motif found in arrays of tandem repeats throughout the genome. Some of these arrays have picked up mutations. I would like to annotate all the arrays in the genome, including degenerate arrays with a lot of mutations. As a first step, I was thinking to perform a pairwise se ...
genome sequence alignment written 8 months ago by dr_bantz50
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Answer: A: Need help about mRNA-Seq result
... cummeRbund (part of the Tuxedo suite) accepts FPKM input. http://compbio.mit.edu/cummeRbund/ ...
written 11 months ago by dr_bantz50
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Comment: C: Error with samtools - indexing alignments: Writing to standard output failed: br
... Sounds like your bam files might be too big. See here: https://www.biostars.org/p/190503/ ...
written 13 months ago by dr_bantz50
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Comment: C: Deseq2 pairwise comparision
... You've missed an apostrophe and a comma in there and the variables in the data frame have different lengths (ie, one of them has the wrong number of samples). ...
written 13 months ago by dr_bantz50
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Answer: A: Deseq2 pairwise comparision
... The 'colData' argument specifies the sample information. This should be a one column dataframe containing the condition for each sample, with the name of the samples as the row names. colData <- data.frame(condition = conditions) row.names(colData) <- names where "conditions" is a ...
written 13 months ago by dr_bantz50
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Comment: C: Deseq2 pairwise comparision
... "paired end" is to do with the technology used for the sequencing itself (I imagine you used single end - either way it's not relevant to your question). The link igor posted gives some guidelines as to how to deal with having samples encompassing multiple variables (conditions/cell lines). You say ...
written 13 months ago by dr_bantz50

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