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Recent Replies
Answer: Parse ncbiRefSeq (other like) annotations
by
vkkodali_ncbi
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3.1k
Not quite a solution to parse UCSCs `ncbiRefSeq.txt.gz` files but if you are interested in RefSeq annotation, you may want to download the …
Answer: Gallery: Computational tools for DNA methylation
by
Naz
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For Analysis: MethylKit ,
For data visualization: SeqMonk
Answer: Read counts an order of magnitude higher on one chromosome
by
ATpoint
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I am neither a RAD-seq person, nor familiar with these organisms but regions that are prone to accumulate excessive read counts are not unc…
Comment: How to generate bam to vcf containing ancestral allele (AA) information?
by
taniamahmood38
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Alright, many thanks for your guidance.
Comment: How to generate bam to vcf containing ancestral allele (AA) information?
by
Ram
36k
I'm not sure how well studied goat is. There was no mention of the organism in your original post so I thought you were referring to human …
Comment: Read counts an order of magnitude higher on one chromosome
by
Michael Dondrup
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Could you do this plot for other chromosomes as well? The peak might be there, too.
Comment: How to generate bam to vcf containing ancestral allele (AA) information?
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taniamahmood38
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Thank you so much for your guidance. Can you please guide me from where can I get the goat's ancestral allele file? Really sorry to bother …
Answer: Read counts an order of magnitude higher on one chromosome
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Michael Dondrup
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Possibly this is not a complete explanation but keep in mind that salmonids have undergone several rounds of whole-genome duplications, see…
Comment: How to filter .fa file by gene_biotype
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jakub
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This may be a duplicate of https://www.biostars.org/p/9524249/#9524252, or the thread may be helpful anyways.
Main question is: why do you …
Answer: How to create bed file from list of variants with indels and bp values
by
Alex Reynolds
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Hope this is useful, if you have the original VCF file:
```
vcf2bed --snvs < variants.vcf > snvs.bed
vcf2bed --insertions < variants.vcf >…
Comment: Adding p value to Vlnplot in Seurat
by
fernandacarneiro.sc
•
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Hi, Antonio!
I'm new at Single Cell and I'm trying to perform an similar analysis with public data on GEO (GSE93374).
In the command `pbmc…
Answer: Read counts an order of magnitude higher on one chromosome
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jv
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> Others have sequenced these species using Rad-seq without this issue so not sure it is biological
Others who? Other researchers in you…
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Why not use following since you already have the accession of the reference sequence.
$ esearch -db nuccore -query NC_000962.3 | elink…
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SeqIO can read and write tab-delimited sequence files and it is my understanding that a TSV file is a tab-delimited file so I'm not sure wh…
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this ended up being correct. I accidentally downloaded the template that didn't have the extra columns to add multiple fastq to one line. t…
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