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Comment: Extracting variant counts from Gnomad genome VCFs
by
Pierre Lindenbaum
135k
what is "a file like this" ? how is it different from a "normal VCF" ?
Comment: Tool to find chromosome specific repeats
by
Michael Dondrup
48k
Thanks for accepting my answer. Coming back to the initial task of coloring chromosomes I have the impression that you want to do [multicol…
Comment: Next Generation Sequencing: in which sequencing technology the read can Not exce
by
lieven.sterck
11k
I see , but then also Sanger should be able to do this, no?
Likely pacbio & nanopore not as the first needs a polymerase to function (and…
Comment: Reference for Salmon
by
ponganta
▴
180
Hi, I have a question: does the result consist of predicted CDS? Because I was wondering whether you can use predicted CDS instead of e.g. …
Comment: Assessing read support for coding sequences predicted by TransDecoder
by
ponganta
▴
180
Yes, they were the only problem encountered. However, I did not use the entire RefSeq-database for annotation, but only one custom database…
Comment: problem in creating an object for a list of fasta files
by
cpad0112
15k
If this is bash script, this is unnecessarily complex. Let us say you have all the fasta files in `test` directory, want to use `ls` for l…
Comment: File conversion from coordinates to genes
by
storm1907
•
0
Hello,
also I was wondering, if it possible to write gene names together with SNP position as well in the 2nd column?
Answer: BioMart servers down again...
by
Michal @Ensembl
▴
110
Hi,
I'm sorry that you've had a problem while using BioMart. BioMart experienced a heavy load yesterday's evening due to a number of large…
Comment: How Do Heterozygotes And Somatic Mutations Manifest In Sequencing Projects
by
ginnyli056
•
0
How to explain a het (0/1) somatic mutation in tumor with VAF higher than 50%? I saw some of these cases in the TCGA vcf files. could it be…
Answer: Existing Glycomics/Glycan databases with sugar modifications?
by
Joe
19k
Answering my own question (but not in a remotely exhaustive or even particularly thorough manner 😅):
- https://unicarb-db.expasy.org/
…
Comment: In need of help with grad school genomic analysis project
by
qmarulfiz
▴
50
I am new in bioinformatic (just involve for about 3 month)
Everything you wrote till the GSEA analysis is similar to my initial plan for t…
Comment: Haplotype Calling Using GATK HaplotypeCaller to Get Exact 35718025 Positions/Loc
by
Pierre Lindenbaum
135k
what is an "accession" ?
Comment: Annotating a genome using a previous annotation file
by
Juke34
★
5.5k
See table5 of this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6450745/ (Whole-Genome Alignment and Comparative Annotation)
Lif…
Comment: Next Generation Sequencing: in which sequencing technology the read can Not exce
by
shelkmike
▴
420
Illumina sequencing machines don't always add "A". I saw more or less random sequences after the adapter. I wasn't able to understand how I…
Comment: Technical single-cell question
by
ATpoint
48k
Hello, what exactly is the question now? You can just count how many cells have counts for that gene > 0 and divide by total cell number. I…
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