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182 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
6 days ago by
vytarasov
▴ 180
1
vote
15
replies
654
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
4 hours ago by
hophuquy0944
• 0
2
votes
14
replies
3.0k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 3 days ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
38
votes
12
replies
31k
views
9 follow
How to systematically check if a bam file is truncated
Exomeseq
updated 18 hours ago by
alanh
▴ 170 • written 7.1 years ago by
jonessara770
▴ 240
0
votes
11
replies
545
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
5 days ago by
Tuck898
• 0
2
votes
11
replies
671
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 day ago by
egascon
• 0
0
votes
9
replies
608
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 2 days ago by
Wayne
★ 2.0k • written 11 days ago by
JACKY
▴ 140
0
votes
9
replies
601
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
2 days ago by
Arton
▴ 10
0
votes
9
replies
352
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
2 days ago by
njornet
▴ 20
4
votes
9
replies
418
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
21 hours ago by
Gabriel R.
★ 2.9k
2
votes
9
replies
706
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 3 days ago by
Pierre Lindenbaum
161k • written 10 days ago by
schmince
• 0
1
vote
8
replies
426
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
updated 5 hours ago by
Alex Reynolds
35k • written 4 days ago by
ntsopoul
▴ 60
2
votes
8
replies
385
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 5 days ago by
Pierre Lindenbaum
161k • written 6 days ago by
Matteo Ungaro
▴ 100
4
votes
7
replies
424
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
4 days ago by
Chen
• 0
0
votes
7
replies
445
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 5 days ago by
Mohamed Abderrahmane
▴ 20 • written 19 days ago by
matteo.levorato
• 0
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 6 days ago by
Ruqaiya
• 0 • written 5.7 years ago by
xiaozhongzhiping
▴ 20
5
votes
7
replies
496
views
RNA seq analysis
DESeq
RNA-seq
3 days ago by
Jacek
▴ 20
6
votes
7
replies
391
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
5 days ago by
sansan_96
▴ 90
4
votes
7
replies
457
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 21 hours ago by
marco.barr
▴ 130 • written 2 days ago by
diqixiaoyaoer
▴ 20
0
votes
7
replies
4.3k
views
B allele frequency (BAF)
snp
updated 6 hours ago by
aidangcruickshank
▴ 10 • written 3.7 years ago by
rthapa
▴ 90
0
votes
6
replies
425
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 4 days ago by
Ram
43k • written 7 days ago by
ajbarrett98
• 0
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 2 days ago by
Ram
43k • written 3.9 years ago by
millere
• 0
2
votes
6
replies
388
views
BWA alignment
Samtools
bam
updated 3 days ago by
a.alnawfal.1992
▴ 260 • written 5 days ago by
Vahid
• 0
0
votes
6
replies
258
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
12 hours ago by
hannes.bongartz
• 0
3
votes
6
replies
491
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 5 days ago by
Pine
▴ 20 • written 12 days ago by
snajafy
• 0
4
votes
5
replies
4.4k
views
Tool:
GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly
Structural-Variation
Variant-Calling
updated 1 day ago by
dario.garvan
▴ 520 • written 7.2 years ago by
d-cameron
★ 2.9k
2
votes
5
replies
497
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 3 days ago by
Ram
43k • written 9 days ago by
Prawesh
• 0
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 5 days ago by
Ruqaiya
• 0 • written 6.7 years ago by
maple964
• 0
1
vote
5
replies
261
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq
deseq2
updated 1 day ago by
Ram
43k • written 2 days ago by
manuelmourato25
• 0
1
vote
5
replies
264
views
Annotating file using bcftools
annotation
plink
bcftools
1 day ago by
kl
▴ 10
1
vote
5
replies
217
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos
atacseq
updated 2 days ago by
Pierre Lindenbaum
161k • written 2 days ago by
biology_inform
▴ 50
0
votes
5
replies
285
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 2 days ago by
GenoMax
142k • written 3 days ago by
chrisk
• 0
1
vote
5
replies
800
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
2
votes
5
replies
578
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 5 days ago by
arctic
▴ 40 • written 14 days ago by
M.
▴ 30
6
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing
coverage
3 days ago by
Arton
▴ 10
1
vote
5
replies
291
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 16 hours ago by
dthorbur
★ 2.0k • written 1 day ago by
BATMAN
• 0
2
votes
5
replies
270
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 4 days ago by
Philipp Bayer
8.5k • written 4 days ago by
林明德
• 0
0
votes
5
replies
319
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
4 days ago by
SilhouetteQ
• 0
0
votes
5
replies
335
views
How to convert normalized BigWig file to count matrix?
count-matrix
BigWig
5 days ago by
feather-W
• 0
2
votes
4
replies
270
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 2 days ago by
yura.grabovska
▴ 90 • written 2 days ago by
ev97
▴ 20
0
votes
4
replies
279
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 1 day ago by
Tony
• 0 • written 2 days ago by
vk
▴ 10
6
votes
4
replies
13k
views
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
trimmomatic
paired-end
updated 6 days ago by
Ruqaiya
• 0 • written 6.5 years ago by
dllopezr
▴ 130
2
votes
4
replies
228
views
Help with IGV abbreviation
igv
updated 3 days ago by
Ram
43k • written 4 days ago by
GeneC
• 0
1
vote
4
replies
342
views
Contig assembly task, errors
dna
genetics
contig
assembly
updated 4 days ago by
Ram
43k • written 9 days ago by
samRayne
• 0
3
votes
4
replies
366
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 1 day ago by
GenoMax
142k • written 2 days ago by
Pierre Lindenbaum
161k
0
votes
4
replies
246
views
calculating genomic coverage/ base overlap in R
genomics
updated 1 day ago by
Ram
43k • written 2 days ago by
Xbox_27
• 0
1
vote
4
replies
282
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
2 days ago by
Arton
▴ 10
2
votes
4
replies
298
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
3 days ago by
Esraa
• 0
0
votes
4
replies
406
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
5 days ago by
beginner123
• 0
0
votes
4
replies
241
views
Sequencing Depth (Read Depth) Calculations
depth
2 days ago by
LucisTheFather
• 0
182 results • Page
1 of 4
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Answer: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
C: How can I perform Differential expression analysis with just one control and one
C: How can I perform Differential expression analysis with just one control and one
C: How can I perform Differential expression analysis with just one control and one
How can I perform Differential expression analysis with just one control and one cancer sample?
Comment: scRNAseq Differential expression analysis
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Recent Replies
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Our resul…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
by
aidangcruickshank
▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2
by
swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot
by
LauferVA
4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot
by
bk11
★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool
by
ntsopoul
▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
Answer: Trimming tool
by
GenoMax
142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
bk11
★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
Comment: Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
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