User: Schmendrick

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Schmendrick10
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1 year, 2 months ago
Joined:
1 year, 8 months ago
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m***********@nhm.ac.uk

Posts by Schmendrick

<prev • 6 results • page 1 of 1 • next >
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Comment: C: How to plot coverage and depth statistics of a bam file
... This is really useful. However on the final step I get an error message from R: Unexpected symbol in "library(lattice, pos=10) xyplot" I can't see an error here but obviously there is one. If anyone has a good eye and has any suggestions to correct this that would be great... ...
written 15 months ago by Schmendrick10
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Calling SNPs across different genome versions
... I'm new to working on genomic level data so was hoping someone could help with this. Sorry if it's a daft question! I have a list of SNPs that I want to call on the cat genome version 8_0. However, the reference locations of these are from a former genome version which is no longer available. The ...
genome snp written 15 months ago by Schmendrick10 • updated 15 months ago by WouterDeCoster26k
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Comment: C: Control Region Annotation
... There are a couple of programs that are fairly good at annotating functional genes and non-coding regions from mitochondrial nucleotide sequences (MITOS is one). They just don't annotate the hypervariable (HV) regions within the non-coding control region. I know there has to be a way to do it becaus ...
written 16 months ago by Schmendrick10
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Answer: A: Control Region Annotation
... Thanks for the replies. I should have been more clear that I'm working with subspecies Felis silvestris silvestris, the European wildcat. There are differences in Control Region length and composition within this subspecies group so its v unlikely that annotations taken from a different species will ...
written 16 months ago by Schmendrick10
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Control Region Annotation
... Hey All, Pretty simple q here but one which I can't seem to solve.... Does anyone know of a mitochondrial genome annotator that will annotate the control region? I've used MITOS for whole mitogenome annotation but it doesn't give details on sub-regions within the CR (hypervariable regions for exam ...
annotation control region written 16 months ago by Schmendrick10
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Finding pre defined SNPs with bedtools
... Bit of a newbie question here... I have a dataset of Illumina paired end reads mapped to a reference genome with BWA. The next step which I'm struggling with is to call SNPs from this dataset from an existing input list of SNPs. I know how to use bedtools to call new SNPs and to quality filter the ...
bedtools samtools bcftools snp written 20 months ago by Schmendrick10 • updated 20 months ago by natasha.sernova2.8k

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