User: Rubal

gravatar for Rubal
Rubal310
Reputation:
310
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Location:
Germany
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2 weeks, 5 days ago
Joined:
8 years, 8 months ago
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Posts by Rubal

<prev • 100 results • page 2 of 10 • next >
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How to generate rainfall plots when using multiple different species assemblies
... I have single nucleotide variant calls in .txt format from individuals from a variety of species. For each sample I have a .txt file with a list of positions in the following format contig start end reference_allele alternative_allele chr1 34 35 A T chr9 667 668 G C For each species al ...
fasta snps visualization genomics written 3 months ago by Rubal310 • updated 3 months ago by bernatgel2.5k
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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 7 months ago by Rubal310
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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 10 months ago by Rubal310
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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 10 months ago by Rubal310 • updated 10 months ago by Pierre Lindenbaum128k
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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 11 months ago by Rubal310 • updated 11 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 12 months ago by Rubal310 • updated 12 months ago by ATpoint35k
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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 12 months ago by Rubal310 • updated 12 months ago by ATpoint35k
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Comment: C: Merge contigs in fasta file
... brilliant thank you ...
written 12 months ago by Rubal310
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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 12 months ago by Rubal310 • updated 12 months ago by finswimmer13k
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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 12 months ago by Rubal310 • updated 12 months ago by finswimmer13k

Latest awards to Rubal

Popular Question 20 months ago, created a question with more than 1,000 views. For Identifying which allele is derived in non-human species
Great Question 2.0 years ago, created a question with more than 5,000 views. For Summarising Whole Genome Allele Frequency Spectrum from VCF file
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Identifying which allele is derived in non-human species
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Best way to compare rate of amino acid change between proteins?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For How to compare the rate of sequence or amino acid evolution between a set of genes?
Popular Question 3.2 years ago, created a question with more than 1,000 views. For How to compare the rate of sequence or amino acid evolution between a set of genes?
Popular Question 3.2 years ago, created a question with more than 1,000 views. For How Can I Divide Snp Data Into Fixed Windows Based On Physical Distance ?
Popular Question 3.2 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
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Interpreting XPEHH output
Student 3.2 years ago, asked a question with at least 3 up-votes. For Summarising Whole Genome Allele Frequency Spectrum from VCF file
Supporter 3.7 years ago, voted at least 25 times.
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Interpreting XPEHH output
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Overlap between 2 sets of genomic regions of differing size
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Detect Regions In A List That Are Within 1 Megabase Of Each Other
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Summarising Whole Genome Allele Frequency Spectrum from VCF file
Popular Question 4.6 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
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Summarising Whole Genome Allele Frequency Spectrum from VCF file
Popular Question 5.3 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
Student 5.3 years ago, asked a question with at least 3 up-votes. For How To Identify Substitutions Between Populations In A Vcf
Popular Question 6.0 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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