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120,847 results • Page
1 of 2417
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Votes
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0
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0
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56
views
Tool:
A rust binding for pairwise/multi sequence aligner: bsalign-rs
bsalign
alignment
10 hours ago by
dwpeng
▴ 110
0
votes
0
replies
47
views
what database should I use for de novo genome in AUGUSTUS
genome
AUGUSTUS
galaxy
annotation
11 hours ago by
Jl
• 0
0
votes
1
reply
205
views
Should I process two complete sets of 10x single-cell multiomics sequencing files from one donor together or separately?
10x_multiome
ENCODE
cellranger_arc
updated 12 hours ago by
GenoMax
150k • written 14 hours ago by
Wu-Sheng Zhang
• 0
835
votes
169
replies
171k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 6 months ago by
Biostar
3.4k • written 8.3 years ago by
Istvan Albert
102k
0
votes
2
replies
130
views
Perform DEGs with pyDESeq2 in CCLE Melanoma Data But Contains Negative Values
DEG
CCLE
Melanoma
pyDESeq2
20 hours ago by
mete.han.celebi
• 0
0
votes
0
replies
79
views
energy minimisation
Energy
updated 1 day ago by
Pierre Lindenbaum
165k • written 1 day ago by
swarnadurga66666m
• 0
0
votes
1
reply
99
views
How to concatenate different domains in the target database identified by hmmsearch
multiple
domains
hmmsearch
updated 1 day ago by
GenoMax
150k • written 1 day ago by
Yongjie Zhang
▴ 110
0
votes
1
reply
104
views
How to filter Hmmsearch alignment
Hmmsearch
updated 19 hours ago by
Mensur Dlakic
★ 29k • written 1 day ago by
Yongjie Zhang
▴ 110
2
votes
3
replies
2.2k
views
Defining residues as buried or exposed based in ASAs/RSAs
structural-bioinformatics
protein-biology
updated 1 day ago by
Dan A
• 0 • written 3.7 years ago by
Agenor Neto
▴ 10
1
vote
1
reply
133
views
Understanding Re-use of Query Sequences in Long Read Alignments
Alignment
PacBio
pbmm2
Minimap2
updated 1 day ago by
LauferVA
4.6k • written 1 day ago by
Charles-Alexandre Roy
▴ 50
0
votes
0
replies
77
views
Question about `vg construct`
vg
1 day ago by
zhengluo
• 0
0
votes
2
replies
187
views
Discrepancy between BAM and vcf
discrepancy
vcf
DRAGEN
updated 1 day ago by
Istvan Albert
102k • written 1 day ago by
louis-gil
• 0
2
votes
1
reply
325
views
Question about `vg giraffe`
vg
updated 1 day ago by
GenoMax
150k • written 3 days ago by
zhengluo
• 0
0
votes
1
reply
415
views
Difference in mapping rate when aligned with mapper.pl of miReep2 and bowtie1
small-RNASeq
miRNASeq
bowtie
miRDeep2
updated 2 days ago by
Ram
45k • written 9 months ago by
MIKA
• 0
1
vote
2
replies
242
views
How to align library of highly similar sequences
MPRA
variant
alignment
BWA
SNV
updated 2 days ago by
ATpoint
87k • written 2 days ago by
rustyshackleford
• 0
0
votes
3
replies
1.5k
views
How to introduce normalized and scaled seurat data into monocle 3?
Monocle
scRNA-seq
Seurat
updated 2 days ago by
Bastien Hervé
6.2k • written 22 months ago by
Sun
• 0
0
votes
0
replies
136
views
Reannotation of complete bacterial genome sequence
re-annotation
genome
whole
Automated
2 days ago by
csag6433
• 0
0
votes
2
replies
695
views
What are the best tools for quantifying allele-specific expression from bulk RNA-seq data these days?
ase
phASER
allele
gene
gatk
updated 2 days ago by
GenoMax
150k • written 2 days ago by
Paulo
• 0
3
votes
4
replies
3.2k
views
Lift over of GWAS summary stat file from Hg38 to Hg19
Hg38
linux
Liftover
GWAS
Hg19
updated 1 day ago by
Mllepnos
• 0 • written 3.8 years ago by
AVA
▴ 40
8
votes
3
replies
276
views
How do I install Terminal on Windows?
Terminal
updated 2 days ago by
5heikki
11k • written 3 days ago by
phyms
• 0
1
vote
1
reply
169
views
Mapping reversion mutations
NGS
reversion
mutation
updated 2 days ago by
Ram
45k • written 3 days ago by
reddyraghuveer664
• 0
0
votes
0
replies
132
views
Issue with Fetching Population Allele Frequency in gnomAD GraphQL API
allelle
frequency
api
GraphQL
gnomad
3 days ago by
DareDevil
★ 4.4k
0
votes
1
reply
171
views
Attempts to demultiplex long reads from .pod5 result in unclassified reads
dorado
sequencing
Long-read
demultiplex
updated 3 days ago by
GenoMax
150k • written 3 days ago by
Placeholder@12654926
• 0
0
votes
1
reply
199
views
Issue with BSgenomeForge::forgeBSgenomeDataPkgFromNCBI
R
BSgenomeForge
BSgenome
NCBI
updated 3 days ago by
ATpoint
87k • written 3 days ago by
noodle
▴ 640
1
vote
1
reply
206
views
Batch effect or biological difference
Batch-effect
updated 2 days ago by
Ram
45k • written 3 days ago by
cynthier
• 0
3
votes
2
replies
251
views
Inconsistency between VCF and HGVS
VEP
3 days ago by
Senanu
▴ 30
0
votes
0
replies
146
views
VCFtools + easySFS snp # discordance
RADtags
vcftools
updated 3 days ago by
GenoMax
150k • written 3 days ago by
laurasachica7
• 0
0
votes
4
replies
3.2k
views
Generating Multiple Alignment Format file (Maf)
maf
multiple-alignment
mafft
updated 3 days ago by
Ram
45k • written 8.3 years ago by
roz_safavi
• 0
3
votes
6
replies
379
views
STAR: Paired alignment gets ~18% unmapped (too short), but single reads get >90% mapping
paired-end
star
rnaseq
2 days ago by
Davor
• 0
1
vote
0
replies
227
views
Job:
bioinformatician position, Ohio State University, Columbus, USA
bioinformatician
updated 3 days ago by
GenoMax
150k • written 3 days ago by
ilaria.palmisano
▴ 10
3
votes
4
replies
307
views
Coverage drop at assembly ends
bowtie2
bw-mem
alignment
minimap2
updated 3 days ago by
GenoMax
150k • written 3 days ago by
alenew.am
▴ 10
1
vote
4
replies
383
views
How to identify additional SNPs on EPICv2
SNPs
methylation
EPIC
3 days ago by
Basti
★ 2.0k
0
votes
1
reply
208
views
jcvi:ValueError: A total of 0 anchor was found. Aborted.
jcvi
Collinearity
updated 3 days ago by
Ram
45k • written 3 days ago by
JieQY
• 0
0
votes
5
replies
420
views
SNPcheck alternative
SNPCheck
updated 4 days ago by
GenoMax
150k • written 4 days ago by
KirGen
▴ 30
0
votes
0
replies
163
views
Comparing HMMER vs. HHrepID for LRR Repeat Detection and Boundary Consistency
hmmer
repeats
4 days ago by
jllPons
• 0
0
votes
0
replies
198
views
circos plot help
visualization
SNV
genomics
circos
updated 2 days ago by
Ram
45k • written 4 days ago by
Genomancer
• 0
2
votes
3
replies
301
views
DAVID List Upload/Gene Conversion Tool
DAVID
updated 3 days ago by
Ram
45k • written 4 days ago by
b5708137
• 0
0
votes
8
replies
3.0k
views
6 follow
CIBERSORTx error: 'x' must be an array of at least two dimensions
matrix
CIBERSORTx
signature
updated 4 days ago by
GenoMax
150k • written 2.7 years ago by
Jie
• 0
1
vote
2
replies
571
views
Can I combine segment results from Sequenza and cnvkit?
CNV
sequenza
cnvkit
4 days ago by
Ram
45k
1
vote
6
replies
432
views
Shotgun dataset with polyG, low qualiity
shotgun-data
updated 2 days ago by
andres.firrincieli
3.9k • written 4 days ago by
shevch2009
• 0
0
votes
2
replies
272
views
MAGeCK: Doing two sided test on gene level?
MAGeCK
4 days ago by
gernophil
▴ 120
0
votes
5
replies
378
views
Is TETranscripts useful for repetitive sequences analysis?
TEtranscripts
updated 4 days ago by
Michael
55k • written 5 days ago by
frarodmar17
• 0
2
votes
5
replies
377
views
SlingShot and Subsetting data
scrna
slingshot
trajectory
updated 2 days ago by
jared.andrews07
★ 18k • written 5 days ago by
carolofharvest
▴ 50
0
votes
1
reply
365
views
Bulk searching UniProt
uniprot
updated 5 days ago by
Elisabeth Gasteiger
★ 2.4k • written 8 days ago by
timothy.kirkwood
▴ 140
4
votes
6
replies
394
views
Problem with Accession Number Changes in UniProt FASTA Sequences
FASTA
Accession
Uniprot
IdMapping
4 days ago by
bioinfo_enthusiast
• 0
1
vote
2
replies
410
views
PPI Network Analysis of Virulence Genes in Morganella morganii Using STRING Database
PPI
STRING
5 days ago by
bioinfo_enthusiast
• 0
15
votes
12
replies
788
views
7 follow
Forum:
Reproducibility Crisis
R-Bioinformatics
updated 3 days ago by
i.sudbery
21k • written 5 days ago by
ParastooA
▴ 20
6
votes
13
replies
7.4k
views
7 follow
Getting sample information from GEO
GEO
NCBI
updated 5 days ago by
DareDevil
★ 4.4k • written 7.9 years ago by
Tom_L
▴ 360
0
votes
3
replies
300
views
How to Close a Phage Genome? Issues with PhageTerm and CheckV Completeness
phage
genome
assembly
PhageTerm
updated 4 days ago by
GenoMax
150k • written 5 days ago by
mail2steff
▴ 70
2
votes
2
replies
297
views
RepBase30.02.fasta.tar.gz
RepBase30.02.fasta.tar.gz
offtopic
updated 5 days ago by
Michael
55k • written 5 days ago by
jupitoy
• 0
120,847 results • Page
1 of 2417
Recent Votes
Splice aware aligner - what does it mean?
Answer: Understanding Re-use of Query Sequences in Long Read Alignments
Comment: SlingShot and Subsetting data
Comment: SlingShot and Subsetting data
Reproducibility Crisis
Comment: Shotgun dataset with polyG, low qualiity
Comment: Batch effect or biological difference
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Recent Replies
Comment: Should I process two complete sets of 10x single-cell multiomics sequencing file
by
GenoMax
150k
It is a little confusing since the same sample can't be included in two rows when demultiplexing the data using `bcl-convert` (which leads …
Comment: How to filter Hmmsearch alignment
by
Mensur Dlakic
★ 29k
I don't know how to help with your main question, as this is an unusual approach. You will probably have to write a custom script. Before y…
Comment: Perform DEGs with pyDESeq2 in CCLE Melanoma Data But Contains Negative Values
by
mete.han.celebi
• 0
Thank you so much for your reply! I will check it now!
Answer: Perform DEGs with pyDESeq2 in CCLE Melanoma Data But Contains Negative Values
by
ATpoint
87k
> negative values for some genes in this CCLE melanoma data. I think it arises since CCLE data is a log2 transformed Nobody can tell you…
Comment: How to concatenate different domains in the target database identified by hmmsea
by
GenoMax
150k
See the answer here as an option -->https://www.biostars.org/p/446822/
Answer: Defining residues as buried or exposed based in ASAs/RSAs
by
Dan A
• 0
I was also interested in this topic recently. What I've tried to do is to fit a 2 component Gaussian mixture model to an array of SASA valu…
Answer: Understanding Re-use of Query Sequences in Long Read Alignments
by
LauferVA
4.6k
@charles , You're right to wonder - even a very thoughtful approach, like yours, will generate some confusion. I'll indicate some "clues" …
Comment: Associating VDJ clonotyping data with scRNA-seq in Seurat
by
garcesj
▴ 50
It's a great workaround. My only question is about just removing the duplicates (`tcr <- tcr[!duplicated(tcr$barcode), ]`). Aren't we losin…
Comment: Discrepancy between BAM and vcf
by
Istvan Albert
102k
I will also say that if you take any variant caller and then look at the corresponding BAM file, you'll find many minor inconsistencies - i…
Comment: Lift over of GWAS summary stat file from Hg38 to Hg19
by
Mllepnos
• 0
Thanks a lot for the recommendation to use bcftools +munge and +liftover instead of UCSC liftOver — I’ll definitely try that!
Comment: Discrepancy between BAM and vcf
by
GenoMax
150k
You could write to Illumina tech support and ask for resources that explain the default parameters for SNP calling/filtering in DRAGEN pipe…
Comment: Error gmx_mmpbsa: LP pseudo-atom is not supported
by
namck
• 0
Hi @bhavya2269, did you find any solution to this? I'm getting a similar error.
Comment: Seeking Guidance on Selecting Control ChIP Sequences for nf-core/chipseq Pipelin
by
mark.ziemann
★ 2.0k
These are not really technical replicates if they simply re-sequenced the same library three times. Resequencing multiplexed libraries on d…
Answer: Difference in mapping rate when aligned with mapper.pl of miReep2 and bowtie1
by
wessel.willemsen
• 0
I had the same problem as you but i solved it by allowing the reads to map to more targets. By default mapper.pl does not allow a read to m…
Comment: How to introduce normalized and scaled seurat data into monocle 3?
by
Bastien Hervé
6.2k
For OP's question, my guess is that they got NA's because `ScaleData` is only called on the `VariableFeatures` found the step before. Try …
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