User: Rubal

gravatar for Rubal
Rubal240
Reputation:
240
Status:
Trusted
Location:
Germany
Last seen:
2 weeks, 3 days ago
Joined:
7 years, 10 months ago
Email:
a********@googlemail.com

Posts by Rubal

<prev • 86 results • page 1 of 9 • next >
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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 17 days ago by Rubal240 • updated 17 days ago by SMK1.8k
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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 9 weeks ago by Rubal240 • updated 9 weeks ago by ATpoint19k
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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 9 weeks ago by Rubal240 • updated 9 weeks ago by ATpoint19k
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Comment: C: Merge contigs in fasta file
... brilliant thank you ...
written 10 weeks ago by Rubal240
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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 10 weeks ago by Rubal240 • updated 10 weeks ago by finswimmer11k
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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 10 weeks ago by Rubal240 • updated 10 weeks ago by finswimmer11k
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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 9 months ago by Rubal240
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Comment: C: VCF input for KaryotypeR
... OK I just added some of it as there are >1000 lines for header due to a large number of contigs ...
written 9 months ago by Rubal240
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Comment: C: VCF input for KaryotypeR
... substantially modified the post for readability and will do this thanks ...
written 9 months ago by Rubal240
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Comment: C: VCF input for KaryotypeR
... Thanks for the help but 'start' is a column of integer values in my table. I think I am inappropriately using the toGranges() function. I feel there must be a straightforward way to convert a vcf to a granges object suitable for karyotypeR and was just wondering if someone could point me to that. ...
written 9 months ago by Rubal240

Latest awards to Rubal

Popular Question 9 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 2.8 years ago, voted at least 25 times.
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