User: Rubal

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Rubal330
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330
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Germany
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2 months ago
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8 years, 12 months ago
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Posts by Rubal

<prev • 103 results • page 1 of 11 • next >
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Comment: C: Variation in proportion of methylated CpGs between human cell types
... Thanks for this informative reply and also for the references, I will look into these. Much appreciated! ...
written 8 weeks ago by Rubal330
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Comment: C: Variation in proportion of methylated CpGs between human cell types
... thanks Ventri, that makes good sense. I come across claims that some stem cells are hypo or hypermethylated but rarely find a statistic for the global methylation of CpGs compared to the approx 70% avg, I'm curious if some human cell types are lower than say 30% methylated CpGs or if hypomethlation ...
written 9 weeks ago by Rubal330
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Variation in proportion of methylated CpGs between human cell types
... Hello Everyone, I am trying to ascertain the extent to which the proportion of methylated CpGs varies between cell types in the human body. I have looked through some of the methylation literature, particularly looking at whole-genome bisulphite sequencing data but have found it challenging to get ...
genome cpgs epigenetics methylation cell written 9 weeks ago by Rubal330 • updated 9 weeks ago by Ventrilocus50
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Make a bed file to exclude 1Mb from start and end of contigs
... I have lists of contig coordinates for several assemblies and would like to create a bed format mask to exclude variants in the first and last 1Mb of each contig. Example lines from the contig files: Chr1 1 123000000 Chr2 1 11435255 AEG1.2 1 2335 I could do something simple using awk ...
genome filter mask bed written 6 months ago by Rubal330 • updated 4 months ago by Biostar ♦♦ 20
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Comment: C: How to create a bed file from a fasta containing all regions with clusters of >=
... haha ok thanks for the quick response! ...
written 6 months ago by Rubal330
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Comment: C: How to create a bed file from a fasta containing all regions with clusters of >=
... The version of seqkit I am using has no -F flag for locate, was this a typo or am I using the wrong version? I just downloaded the latest version from thttps://bioinf.shenwei.me/seqkit/download/ ...
written 6 months ago by Rubal330
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Comment: C: How to create a bed file from a fasta containing all regions with clusters of >=
... brilliant I will give this a try ...
written 6 months ago by Rubal330
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How to create a bed file from a fasta containing all regions with clusters of >= 50 Ns and flanking 1kb regions
... From a genome fasta file I would like create a bed file containing the start and end coordinates of all runs of >= 50 Ns, such as this: ATGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAATCC and 1kb of flanking sequence on either side. So for example if there were 100 consecutive Ns at ...
genome bed filtering fasta written 6 months ago by Rubal330 • updated 6 months ago by ATpoint38k
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Comment: C: Find mutations that are spatially clustered?
... thank you very much for this! ...
written 6 months ago by Rubal330
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Comment: C: Find mutations that are spatially clustered?
... Also something conceptual I don't understand, the code can output a single mutation for a chromosome but if mutations are spatially clustered then by definition there must be at least 2 mutations that are close together. Is this just giving the first mutation if 2 mutations are < 1kb apart? I wou ...
written 6 months ago by Rubal330

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