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20 results • Page
1 of 1
Sort: replies
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Views
Votes
Replies
0
votes
9
replies
549
views
Using VEP annotation output as the input for a second VEP annotation
VCF
VEP
Annotation
updated 11 minutes ago by
Ram
43k • written 3 months ago by
Arton
• 0
4
votes
7
replies
462
views
RNA seq analysis
DESeq
RNA-seq
12 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 19 hours ago by
Juke34
8.6k • written 2 days ago by
Vijith
▴ 30
0
votes
3
replies
107
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
10 hours ago by
Esraa
• 0
0
votes
2
replies
161
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
13 hours ago by
melissa.joubert
• 0
0
votes
2
replies
82
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
meta
how-to
ncbi
forum
3 hours ago by
hophuquy0944
• 0
0
votes
1
reply
103
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 7 hours ago by
Joe
21k • written 17 hours ago by
iqra
• 0
0
votes
1
reply
96
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 9 hours ago by
GenoMax
142k • written 14 hours ago by
chrisk
• 0
0
votes
1
reply
120
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
17 hours ago by
sansan_96
▴ 90
0
votes
1
reply
70
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
4 hours ago by
asalimih
▴ 60
0
votes
1
reply
74
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 4 hours ago by
yura.grabovska
▴ 70 • written 4 hours ago by
ev97
▴ 20
0
votes
0
replies
18
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
1 hour ago by
mgranada3
▴ 30
0
votes
0
replies
68
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
19 hours ago by
brunofelicianodeomena
• 0
0
votes
0
replies
58
views
ReactomeGSA
ReactomeGSA
12 hours ago by
Shaimaa Gamal
▴ 10
0
votes
0
replies
72
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 18 hours ago by
GenoMax
142k • written 19 hours ago by
Dude
• 0
0
votes
0
replies
50
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
7 hours ago by
Lélé
▴ 10
0
votes
0
replies
59
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 6 hours ago by
ATpoint
82k • written 7 hours ago by
yura.grabovska
▴ 70
0
votes
0
replies
49
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
5 hours ago by
jway
• 0
0
votes
0
replies
34
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 2 hours ago by
GenoMax
142k • written 3 hours ago by
Rodolfo Adrián
• 0
0
votes
0
replies
19
views
Add line under stat test
stats
R
1 hour ago by
Ghada
• 0
20 results • Page
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Answer: Calculate allelic frequency from VEP output vcf file
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Recent Replies
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
▴ 110
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
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swbarnes2
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
• 0
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…
Comment: calculating genomic coverage/ base overlap in R
by
marco.barr
▴ 110
The code seems correct at first glance... How did you generate the data in the Excel file? Have you checked the exon annotations? You could…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Did you remeber to unzip/untar the `nt` preformatted files that you downloaded?
Comment: Genotyping sites with N in reference genome
by
shpak.max
▴ 50
Just to clarify, I have set additional sites in the reference genome to 'N', which means (based on your statement) that these will not be g…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Pierre Lindenbaum
161k
see https://www.biostars.org/p/9496674/ <!-- when i runed blastn(version 2.15) and nt database(latest version). I used aspera to download…
Answer: Genotyping sites with N in reference genome
by
Pierre Lindenbaum
161k
> Does UnifiedGenotyper skip/ignore sites where the reference genotype is N yes. The variant is in YOUR data, not in the reference where '…
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