User: dr_bantz

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dr_bantz50
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Posts by dr_bantz

<prev • 17 results • page 1 of 2 • next >
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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 6 weeks 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 4 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 6 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 6 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 6 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 6 months ago by dr_bantz50
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Answer: A: Huge matrix memory issue
... Thanks for all the suggestions! In the end I went for a row-by-row appraoch, as suggested by Jean-Karim Heriche karl.stamm. Using this approach as it is would take 10 days to run on the cluster. However, the approach has some helpful advantages, one of which being that I am now able to embarrassing ...
written 8 months ago by dr_bantz50
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Comment: C: Huge matrix memory issue
... Each i,jth cell would contain the number of times gene i and gene j are mutated in the same train, so this would be have to be computed. The plan is to then make a second matrix with the Poisson probability for the value i,j based on the occurrence of mutation in gene i and j. Your parallelization i ...
written 8 months ago by dr_bantz50
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Huge matrix memory issue
... Hi everyone, I have a WGS dataset consisting of ~2000 samples. I want to look at the co-occurrence of mutations (ie. how often a given pair of genes is mutated in the same strain). The way I'm doing this requires the creation of a 30,000 X 30,000 matrix to represent all pairwise comparisons of gen ...
genome written 8 months ago by dr_bantz50
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Comment: C: Python script to trim 3' A nucleotides running slow
... Awesome, it's turbo-fast now! I just had to add an extra '\n' at the end of the f.write statement (and of course I added fqFile = open(in_file, 'r') before the for loop). Thanks a lot! ...
written 19 months ago by dr_bantz50

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