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22 results • Page
1 of 1
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Votes
Replies
0
votes
0
replies
7
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
cell
RNA
single
ambient
12 minutes ago by
txema.heredia
▴ 110
0
votes
0
replies
26
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
1 hour ago by
Jsarria.EEAD
• 0
0
votes
1
reply
56
views
How can I calculate the OS of each patient?
overall-survival
updated 2 hours ago by
ATpoint
82k • written 2 hours ago by
Pedro
• 0
0
votes
0
replies
28
views
cat-bgen fail
bgenix
updated 2 hours ago by
Ram
43k • written 2 hours ago by
lambard
• 0
0
votes
0
replies
51
views
API kegg - IndexError: list index out of range
kegg
API
Error
8 hours ago by
mirwa.zidi93
• 0
0
votes
0
replies
54
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
10 hours ago by
ebertomeup
• 0
0
votes
1
reply
94
views
Sam file Header problem
Sam
Header
problem
file
updated 10 hours ago by
Pierre Lindenbaum
161k • written 11 hours ago by
saifulislam99121
• 0
0
votes
0
replies
62
views
select set of intervals that cover a genomic region
GRanges
bed
13 hours ago by
ntsopoul
▴ 60
0
votes
0
replies
58
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
15 hours ago by
Luqman
• 0
1
vote
3
replies
156
views
ggrepel function: geom_text_repel()
ggrepel
ggplo2
R
9 hours ago by
sooni
▴ 20
0
votes
2
replies
126
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
10 hours ago by
mavy
▴ 10
0
votes
1
reply
115
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
updated 8 hours ago by
Michael
54k • written 21 hours ago by
mgranada3
▴ 30
0
votes
0
replies
74
views
Add line under stat test
stats
R
21 hours ago by
Ghada
• 0
0
votes
0
replies
74
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 23 hours ago by
GenoMax
142k • written 1 day ago by
Rodolfo Adrián
• 0
2
votes
4
replies
184
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
1 hour ago by
ev97
▴ 20
1
vote
12
replies
343
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
just now by
hophuquy0944
• 0
0
votes
1
reply
127
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 6 hours ago by
Papyrus
★ 2.9k • written 1 day ago by
yura.grabovska
▴ 90
0
votes
1
reply
117
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
updated 3 hours ago by
GenoMax
142k • written 1 day ago by
Lélé
▴ 10
0
votes
5
replies
270
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 16 hours ago by
GenoMax
142k • written 1 day ago by
chrisk
• 0
0
votes
2
replies
159
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 6 hours ago by
DGTool
▴ 20 • written 1 day ago by
iqra
• 0
1
vote
2
replies
188
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
1 hour ago by
bioinfo
▴ 150
0
votes
9
replies
594
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
20 hours ago by
Arton
▴ 10
22 results • Page
1 of 1
Recent Votes
A: How count reads
Answer: Probe annotation file for microarray platform MoGene-1_0-st-v1
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
C: Splitting .vcf file
Answer: Grouping datasets in Seurat
Answer: How should I make kallisto indexes?
Comment: Why does assigning genes with biomart give me different values than using a tran
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Recent Awards •
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Popular Question
to
carlopecoraro2
★ 2.5k
Scholar
to
GenoMax
142k
Popular Question
to
ben@f
▴ 20
Popular Question
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Jalil Sharif
▴ 80
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biology_inform
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Recent Replies
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
by
diqixiaoyaoer
▴ 10
Ok, I will response to you here as soon as possible.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
How much memory do you have available? For `nt` database you are going to need 30-40G minimum. You may simply be running out of memory.
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
by
ev97
▴ 20
Noted! Thanks very much for your help!
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i'm using linux. I was use 3 file.fasta to debug and it is nucleotide file, and my blast -h still work > (/data/quyho/tools/mgs2amr_tool…
Answer: Details on salmon index
by
Rob
6.5k
Hi Lorenzo, Thanks for your question. First, I'd like to clarify that several substantial updates have been made to salmon since its …
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
by
yura.grabovska
▴ 90
sc/snRNASeq tends to have differences in things like mitochondrial genes etc, which you can account for using tools like SCTransform but in…
Comment: Why does assigning genes with biomart give me different values than using a tran
by
bioinfo
▴ 150
Thank you! I ended up using the transcripts_to_genes instead of biomart.
Comment: How can I calculate the OS of each patient?
by
ATpoint
82k
Please be specific. Which TCGA subset, what did you try? Show code.
Answer: mitochondrial genome assembly pipeline
by
shelkmike
★ 1.2k
A good tool for mitochondrial genome assembly is GetOrganelle (https://github.com/Kinggerm/GetOrganelle)
Comment: getting exon coordinates
by
Ram
43k
Please do not use `bioinformatics` as a tag unless your post in about the field of bioinformatics itself.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Ram
43k
I've removed unneccessary tags - `meta` and `how-to` don't apply to this post at all, and the `forum` tag is not in use anymore.
Comment: Difference in number of reads when using duplex and simplex base calling with Do
by
GenoMax
142k
I assume you have posted this in nanopore community and/or on the dorado issues page on GitHub. Please come back and post an update once yo…
Comment: Annotating file using bcftools
by
kl
▴ 10
Do you know if there is a way to leave chr:pos in ID if there is no matching rsid based on chromosome and position, as variants have been r…
Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
by
Jeremy Leipzig
22k
We get this question like clockwork every 6 weeks. I'll say it one more time: **A freeze is a freeze.** Patches are not a thing th…
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
by
ev97
▴ 20
Thanks very much for your feedback! I will take all those things in consideration once I start the analysis! Just out of curiosity, do yo…
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