User: Rubal

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Rubal250
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Germany
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8 years, 1 month ago
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Posts by Rubal

<prev • 89 results • page 1 of 9 • next >
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Comment: C: Modify reference fasta using bed file
... this works well thank you! I am trying to run it changing over a million positions in a 2gb fasta file. Do you recommend any change in approach for this? I'm a little concerned as it produces no intermediate output that I can't tell how long it will take. For example would sorting the example.bed sp ...
written 4 weeks ago by Rubal250
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Comment: C: Calculating effective coverage/callable genome for variant calling from a bam fi
... Thanks very much Pierre, I'll give this a go! For clarificaiton will this only result in a list of regions or will it also give the effective coverage at each site? ...
written 3 months ago by Rubal250
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Calculating effective coverage/callable genome for variant calling from a bam file
... We have mapped whole-genome sequence data in bam format. We are testing a variety of variant callers to identify mutant sites. The variant callers we are using have various different filters that results in sites being excluded from variant calling. For example some variant callers require >=3 re ...
genome variant-calling bam bigwig coverage written 3 months ago by Rubal250 • updated 3 months ago by Pierre Lindenbaum124k
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Modify reference fasta using bed file
... Hello Everyone, I would like to modify a reference genome fasta file using a list of position in bed file format. The bed file contains positions like this: chr1 17716 C G chr1 17925 A G chr1 18115 C T So for example I would like to change the position ...
fasta bed genome written 4 months ago by Rubal250 • updated 4 months ago by SMK1.9k
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Comment: C: How to find total size of regions NOT in bigWig file
... As an alternative to `seqtk` could I also use: `grep -v ">" file.fasta | wc | awk '{print $3-$1}'` ...
written 6 months ago by Rubal250 • updated 6 months ago by ATpoint25k
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How to find total size of regions NOT in bigWig file
... Hello All, I would like to calculate the 'callable genome'. I have a reference genome in fasta format and a bed file with a list of genome coordinates that were excluded from variant calling. Could anybody advise on how to combine these two files to calculate how many sites in the reference genome ...
fasta bed genome written 6 months ago by Rubal250 • updated 6 months ago by ATpoint25k
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Comment: C: Merge contigs in fasta file
... brilliant thank you ...
written 6 months ago by Rubal250
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Comment: C: Merge contigs in fasta file
... Thanks for this. Unfortunately when I save the file and try to run the script as suggested it only shows the awk help manual. It doesn't seem to recognise the -i option? The first lines of what is printed: Usage: awk [POSIX or GNU style options] -f progfile [--] file ... Usage: awk [POSIX o ...
written 6 months ago by Rubal250 • updated 6 months ago by finswimmer12k
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Merge contigs in fasta file
... Hello All, I am running variant calling on some species whose reference genomes have a very high number of contigs (sometimes >400,000). The variant caller I am using splits the job by the number of chromosomes, and is overwhelmed when this number is too high. Therefore I would like to concatena ...
fasta merge contigs written 6 months ago by Rubal250 • updated 6 months ago by finswimmer12k
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Comment: C: VCF input for KaryotypeR
... Thanks the code. When I try with this commandL kpPlotRainfall(kp, data = tmp.vcf.data , col=variant.colors) I get the error: Error in attr(x, "tsp") <- c(1, NROW(x), 1) : attempt to set an attribute on NULL I suspect this is related to needing to create a correct contig base plot for adding th ...
written 13 months ago by Rubal250

Latest awards to Rubal

Popular Question 13 months ago, created a question with more than 1,000 views. For Identifying which allele is derived in non-human species
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Supporter 3.1 years ago, voted at least 25 times.
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Interpreting XPEHH output
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Popular Question 5.4 years ago, created a question with more than 1,000 views. For Where To Find A Good Estimate Of The Background Mutation Rate In Rattus Norvegicus

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