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22 results • Page
1 of 1
Sort: replies
Rank
Views
Votes
Replies
0
votes
9
replies
572
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
2 hours ago by
Arton
▴ 10
4
votes
7
replies
464
views
RNA seq analysis
DESeq
RNA-seq
15 hours ago by
Jacek
▴ 10
1
vote
4
replies
329
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 22 hours ago by
Juke34
8.6k • written 2 days ago by
Vijith
▴ 30
0
votes
3
replies
121
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
10 minutes ago by
chrisk
• 0
0
votes
3
replies
111
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
13 hours ago by
Esraa
• 0
0
votes
2
replies
164
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
16 hours ago by
melissa.joubert
• 0
0
votes
2
replies
98
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
meta
how-to
ncbi
forum
6 hours ago by
hophuquy0944
• 0
0
votes
1
reply
106
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 10 hours ago by
Joe
21k • written 20 hours ago by
iqra
• 0
0
votes
1
reply
86
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 7 hours ago by
yura.grabovska
▴ 70 • written 7 hours ago by
ev97
▴ 20
0
votes
1
reply
124
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
20 hours ago by
sansan_96
▴ 90
0
votes
1
reply
79
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
7 hours ago by
asalimih
▴ 60
0
votes
0
replies
55
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
8 hours ago by
jway
• 0
0
votes
0
replies
72
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
22 hours ago by
brunofelicianodeomena
• 0
0
votes
0
replies
66
views
ReactomeGSA
ReactomeGSA
15 hours ago by
Shaimaa Gamal
▴ 10
0
votes
0
replies
57
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
10 hours ago by
Lélé
▴ 10
0
votes
0
replies
41
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 5 hours ago by
GenoMax
142k • written 6 hours ago by
Rodolfo Adrián
• 0
0
votes
0
replies
35
views
Add line under stat test
stats
R
4 hours ago by
Ghada
• 0
0
votes
0
replies
35
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
4 hours ago by
mgranada3
▴ 30
0
votes
0
replies
77
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 21 hours ago by
GenoMax
142k • written 22 hours ago by
Dude
• 0
0
votes
0
replies
22
views
How to extract cells of different species after mapping with combined genome?
snrnaseq
scrnaseq
2 hours ago by
vk
▴ 10
0
votes
0
replies
16
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
1 hour ago by
mavy
▴ 10
0
votes
0
replies
64
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 9 hours ago by
ATpoint
82k • written 10 hours ago by
yura.grabovska
▴ 70
22 results • Page
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Answer: Calculate allelic frequency from VEP output vcf file
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Recent Replies
Comment: bbmerge (bbmap) ~ error with insert size file output
by
chrisk
• 0
Hi Genomax, This is the thread: https://www.biostars.org/p/9582467/ Cheers, Chris
Comment: Inquiry about deseq2 transformation
by
Chen
• 0
that's helpful, thanks :)
Comment: bbmerge (bbmap) ~ error with insert size file output
by
Brian Bushnell
20k
Ah, this is a little embarrassing; those are the vectors for the neural network. I overloaded a field that was being used for the insert s…
Comment: Annotating file using bcftools
by
kl
▴ 10
Thanks - I corrected it. It doesn't seem to annotate. I converted to binary after which is what is shown below. It is not the output I want…
Comment: Filtering VCF files based on VAF giving incorrect results
by
Arton
▴ 10
These are valid questions. Does your code address the concerns you've raised? From what I understand, FilterVcf is primarily designed for h…
Answer: Calculate allelic frequency from VEP output vcf file
by
ramiro.barrantes
• 0
Found the answer here!! https://github.com/Illumina/strelka/blob/master/docs/userGuide/README.md#somatic Although this leads to a str…
Comment: Using VEP annotation output as the input for a second VEP annotation
by
Ram
43k
That's not a valid reason to delete the post. If that information was sensitive, posting it here was a mistake in the first place. I don't …
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
by
marco.barr
▴ 120
Hi, regardless of how you generated the data whether with DESeq2 or other pipeline, your differential expression matrix can be used as inpu…
Comment: Filtering VCF files based on VAF giving incorrect results
by
Pierre Lindenbaum
161k
> Do you think my commands were correct? I'm not familiar enough with this bcftools syntax. but what if there is no AD, what if both…
Answer: How can you *consistently* download BioProject IDs from NCBI's BioSample databas
by
Ash
▴ 10
I know this was asked several years ago, but finding this post helped me solve my own problem and in the process I solved this one too. …
Answer: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
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14k
Would Parkinson's be expected to have an effect on blood cells? Neurons, sure, but blood cells?
Comment: Doubt about the process of annotation, detection, identification and classificat
by
MarcosCosta
• 0
Thank you very much, you've helped me a lot. Could you suggest a book or article that offers a complete explanation of these processes?
Comment: Filtering VCF files based on VAF giving incorrect results
by
Arton
▴ 10
Thank you. I can't try a completely new tool but I will keep your command for future use. Do you think my commands were correct? For exampl…
Comment: Add stats to boxplot in R
by
Ghada
• 0
Thanks. Thats work
Comment: Genotyping sites with N in reference genome
by
Zhenyu Zhang
★ 1.2k
Whether N -> A/T/G/C represents a variant is heavily dependent on the tool itself, and I know most tools don't. Since you don't see it in y…
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