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184 results • Page
1 of 4
Sort: replies
Rank
Views
Votes
Replies
9
votes
23
replies
9.8k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
5 days ago by
vytarasov
▴ 180
1
vote
14
replies
585
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
3 hours ago by
hophuquy0944
• 0
2
votes
14
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 2 days ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation
reference panel
updated 6 days ago by
analyst
▴ 50 • written 6.4 years ago by
David_emir
▴ 490
0
votes
11
replies
533
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
4 days ago by
Tuck898
• 0
2
votes
11
replies
571
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio
DEG
limma
1 hour ago by
egascon
• 0
0
votes
9
replies
342
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
1 day ago by
njornet
▴ 20
2
votes
9
replies
694
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 2 days ago by
Pierre Lindenbaum
161k • written 9 days ago by
schmince
• 0
0
votes
9
replies
597
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
1 day ago by
Arton
▴ 10
1
vote
9
replies
392
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 6 days ago by
i.sudbery
19k • written 9 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
9
replies
595
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 1 day ago by
Wayne
★ 2.0k • written 10 days ago by
JACKY
▴ 140
2
votes
8
replies
375
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 4 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
Matteo Ungaro
▴ 100
1
vote
7
replies
379
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
2 days ago by
ntsopoul
▴ 60
4
votes
7
replies
398
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
3 days ago by
Chen
• 0
6
votes
7
replies
385
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
4 days ago by
sansan_96
▴ 90
5
votes
7
replies
484
views
RNA seq analysis
DESeq
RNA-seq
2 days ago by
Jacek
▴ 20
0
votes
7
replies
426
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 4 days ago by
Mohamed Abderrahmane
▴ 20 • written 17 days ago by
matteo.levorato
• 0
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 5 days ago by
Ruqaiya
• 0 • written 5.7 years ago by
xiaozhongzhiping
▴ 20
3
votes
7
replies
273
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
updated 1 hour ago by
DGTool
▴ 20 • written 19 hours ago by
Gabriel R.
★ 2.9k
2
votes
6
replies
1.9k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML
ncbi
entrez-direct
updated 1 day ago by
Ram
43k • written 3.9 years ago by
millere
• 0
0
votes
6
replies
419
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 3 days ago by
Ram
43k • written 6 days ago by
ajbarrett98
• 0
2
votes
6
replies
380
views
BWA alignment
Samtools
bam
updated 2 days ago by
a.alnawfal.1992
▴ 260 • written 4 days ago by
Vahid
• 0
3
votes
6
replies
488
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 4 days ago by
Pine
▴ 20 • written 11 days ago by
snajafy
• 0
6
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing
coverage
2 days ago by
Arton
▴ 10
2
votes
5
replies
567
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 4 days ago by
arctic
▴ 40 • written 13 days ago by
M.
▴ 30
2
votes
5
replies
266
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 3 days ago by
Philipp Bayer
8.5k • written 3 days ago by
林明德
• 0
0
votes
5
replies
316
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
3 days ago by
SilhouetteQ
• 0
0
votes
5
replies
277
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 1 day ago by
GenoMax
142k • written 2 days ago by
chrisk
• 0
1
vote
5
replies
783
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 4 days ago by
Ruqaiya
• 0 • written 6.7 years ago by
maple964
• 0
1
vote
5
replies
214
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos
atacseq
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
biology_inform
▴ 50
2
votes
5
replies
491
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 2 days ago by
Ram
43k • written 8 days ago by
Prawesh
• 0
1
vote
5
replies
220
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq
deseq2
updated 10 hours ago by
Ram
43k • written 23 hours ago by
manuelmourato25
• 0
1
vote
5
replies
256
views
Annotating file using bcftools
annotation
plink
bcftools
18 hours ago by
kl
▴ 10
4
votes
5
replies
4.3k
views
Tool:
GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly
Structural-Variation
Variant-Calling
updated 9 hours ago by
dario.garvan
▴ 520 • written 7.2 years ago by
d-cameron
★ 2.9k
0
votes
5
replies
330
views
How to convert normalized BigWig file to count matrix?
count-matrix
BigWig
4 days ago by
feather-W
• 0
1
vote
4
replies
340
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 2 days ago by
Juke34
8.6k • written 3 days ago by
Vijith
▴ 30
0
votes
4
replies
300
views
Correlation Analysis
statistics
methylation
NGS
expression
6 days ago by
Researcher
▴ 30
0
votes
4
replies
2.3k
views
MGLTools does not work in windows 11
windows-11
Autodock
windows
MGLTools
updated 2 days ago by
Ram
43k • written 13 months ago by
mohyeddine.taleb
• 0
0
votes
4
replies
229
views
Sequencing Depth (Read Depth) Calculations
depth
1 day ago by
LucisTheFather
• 0
1
vote
4
replies
277
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
1 day ago by
Arton
▴ 10
2
votes
4
replies
218
views
Help with IGV abbreviation
igv
updated 2 days ago by
Ram
43k • written 3 days ago by
GeneC
• 0
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 3 days ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 0
1
vote
4
replies
339
views
Contig assembly task, errors
dna
genetics
contig
assembly
updated 3 days ago by
Ram
43k • written 8 days ago by
samRayne
• 0
2
votes
4
replies
254
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 1 day ago by
yura.grabovska
▴ 90 • written 1 day ago by
ev97
▴ 20
1
vote
4
replies
283
views
Add stats to boxplot in R
stats
R
1 day ago by
Ghada
• 0
1
vote
4
replies
412
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 6 days ago by
GenoMax
142k • written 29 days ago by
aniigodwinn
• 0
0
votes
4
replies
396
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
4 days ago by
beginner123
• 0
0
votes
4
replies
257
views
Galaxy StringTie error
stringtie
galaxy
2 days ago by
trkfs
• 0
1
vote
4
replies
499
views
cellranger error message
multiplexing
cellranger
updated 6 days ago by
Max
• 0 • written 3 months ago by
Alivia
▴ 10
184 results • Page
1 of 4
Recent Votes
Comment: How does FindNeighbors() and FindClusters() related and work?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
lncRNA and ncPEPs identification
Answer: Identifying common DEGs among multiple datasets
Answer: ggrepel function: geom_text_repel()
Comment: switch off warning in blast command line
Forward And Reverse Strand Conventions
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Recent Replies
Answer: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Having duplicate gene symbols is pretty common. Why do you need to work with gene symbols? To compare them to external datasets? Or just fo…
Comment: Merge clusters in Seurat UMAP
by
kilcdincer
▴ 10
It did not help either. But I got the answer [here][1] Thank you! [1]: https://github.com/satijalab/seurat/issues/8902
Comment: How to generate table_annovar from VCF input?
by
Pierre Lindenbaum
161k
there is no `--allsample` option in the "usage" screen you're showing. I suspect you're using an old version ?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
egascon
• 0
Thank you very much again. I have learned a lot of things.
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
egascon
• 0
It's a microarryay experiment, not RNASeq
Comment: Sam file Header problem
by
Pierre Lindenbaum
161k
https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
DGTool
▴ 20
I have also recently come across another global alignment algorithm that was recently released which could seem pretty interesting to test …
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
b.contreras.moreira
▴ 190
Not sure, you might ask in the repo, please share here the response if you find it
Comment: How to generate table_annovar from VCF input?
by
LucisTheFather
• 0
Would you be more specific to your question? Do you mean how to debug this syntax error?
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
thank you
Comment: How to extract cells of different species after mapping with combined genome?
by
Tony
• 0
I think this method should be applicable to all high-throughput single-cell RNA-seq platforms. Although the method of determining cell spec…
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Nyksubuz
▴ 10
The dataset you want (taestivum_eg_gene) exists within the "plants_mart" schema, not the default schema. Your current code assumes the defa…
Comment: Add line under stat test
by
Nyksubuz
▴ 10
You could use [this][1] [1]: https://ggplot2.tidyverse.org/reference/geom_segment.html
Comment: API kegg - IndexError: list index out of range
by
Nyksubuz
▴ 10
It might be because the gene symbol is not found in the KEGG database. Add some extra error handling before parsing the results or do a man…
Comment: Sam file Header problem
by
saifulislam99121
• 0
Thank you for your reply. I am not very much sure about this RG. Can you explain me a bit?
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