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1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
1
vote
4
replies
293
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 4 hours ago by
Juke34
8.6k • written 1 day ago by
Vijith
▴ 30
0
votes
1
reply
147
views
consensus sequence calling
consensus
updated 1 day ago by
bk11
★ 2.4k • written 1 day ago by
Ghada
• 0
0
votes
3
replies
171
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 1 day ago by
Ram
43k • written 1 day ago by
yau
• 0
3
votes
2
replies
257
views
imputation through beagle
panel
beagle
reference
imputation
22 hours ago by
analyst
▴ 50
0
votes
0
replies
83
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
1 day ago by
JACKY
▴ 140
0
votes
1
reply
488
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
updated 1 day ago by
aw7
▴ 280 • written 25 days ago by
abhishekghadge
• 0
1
vote
1
reply
198
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
updated 1 day ago by
aw7
▴ 280 • written 6 days ago by
Zeng Hao
▴ 40
0
votes
0
replies
96
views
Reference panel of normals for ensembl named refgenome
Mutect2
1 day ago by
gernophil
▴ 80
1
vote
0
replies
90
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
1 day ago by
tomas4482
▴ 400
2
votes
6
replies
296
views
BWA alignment
Samtools
bam
updated 12 minutes ago by
a.alnawfal.1992
▴ 260 • written 2 days ago by
Vahid
• 0
3
votes
2
replies
176
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 1 day ago by
ATpoint
82k • written 1 day ago by
jennyp0706
• 0
0
votes
1
reply
150
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence
university
assembly
protein
genomics
updated 1 day ago by
Philipp Bayer
8.5k • written 2 days ago by
samRayne
• 0
0
votes
1
reply
233
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 1 day ago by
Ram
43k • written 5 days ago by
Nikki
• 0
2
votes
14
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 18 hours ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
0
votes
1
reply
184
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
updated 2 days ago by
chrchang523
10k • written 7 days ago by
analyst
▴ 50
0
votes
0
replies
100
views
lncRNA
tcga
lncrna
2 days ago by
jain72744
▴ 10
0
votes
1
reply
228
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
updated 2 days ago by
Zhenyu Zhang
★ 1.2k • written 5 days ago by
jain72744
▴ 10
2
votes
5
replies
541
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 2 days ago by
arctic
▴ 40 • written 11 days ago by
M.
▴ 30
1
vote
2
replies
344
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq
limma
RNA-seq
removeBatchEffect
batch-effect
updated 1 day ago by
Ram
43k • written 2 days ago by
t.fortunato.asquini
• 0
2
votes
1
reply
242
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
updated 2 days ago by
pjb39
▴ 210 • written 4 days ago by
beantkapoor16
▴ 10
0
votes
2
replies
195
views
Output file of samtools flagstat empty
samtools-flagstat
updated 1 day ago by
colindaven
6.4k • written 2 days ago by
ramendra.sarma
• 0
0
votes
0
replies
103
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
eigencorplot
PCAtools
deseq2
pca
2 days ago by
BioinfGuru
★ 1.7k
2
votes
8
replies
341
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 2 days ago by
Pierre Lindenbaum
161k • written 2 days ago by
Matteo Ungaro
▴ 100
0
votes
0
replies
119
views
News:
Online course: An Introduction to Nanopore Direct RNA Sequencing
Nanopore
RNAseq
2 days ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
224
views
input file in rmats
rmats
updated 3 days ago by
Mathew
▴ 140 • written 4 days ago by
Lambodarswain316
• 0
3
votes
3
replies
329
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 1 day ago by
Mathew
▴ 140 • written 4 days ago by
Christopher
• 0
6
votes
7
replies
362
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
2 days ago by
sansan_96
▴ 90
2
votes
3
replies
256
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio
Cibersort
R
1 day ago by
Azra
▴ 10
2
votes
1
reply
223
views
Failed to open VCF file
GATK
sentieon
BWA-MEM
updated 3 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
melissachua90
▴ 70
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 3 days ago by
Ruqaiya
• 0 • written 5.7 years ago by
xiaozhongzhiping
▴ 20
0
votes
4
replies
372
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
1 day ago by
beginner123
• 0
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 3 days ago by
Ruqaiya
• 0 • written 6.4 years ago by
dllopezr
▴ 130
0
votes
2
replies
222
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
1 day ago by
analyst
▴ 50
0
votes
6
replies
391
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 1 day ago by
Ram
43k • written 4 days ago by
ajbarrett98
• 0
0
votes
11
replies
506
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
2 days ago by
Tuck898
• 0
3
votes
3
replies
267
views
what is another word for a BLAST "hit"?
blast
alignment
4 days ago by
dec986
▴ 380
0
votes
1
reply
194
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 4 days ago by
Ram
43k • written 4 days ago by
Shwetha
• 0
0
votes
0
replies
158
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 4 days ago by
Ram
43k • written 4 days ago by
naomiboldon
• 0
1
vote
3
replies
271
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 4 days ago by
Ram
43k • written 4 days ago by
Omics data mining
▴ 260
1
vote
7
replies
598
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 4 days ago by
Pierre Lindenbaum
161k • written 7 days ago by
schmince
• 0
0
votes
5
replies
303
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
1 day ago by
SilhouetteQ
• 0
0
votes
1
reply
179
views
Alignment of samples with spike-in
alignment
multimapping
RNA-seq
ChIP-seq
spike-in
updated 4 days ago by
GenoMax
142k • written 4 days ago by
maria.soler
• 0
0
votes
2
replies
279
views
How are score_weights calculated in this code?
single-cell
3 days ago by
carolofharvest
▴ 40
0
votes
1
reply
215
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
updated 4 days ago by
curious
▴ 750 • written 4 days ago by
SeoGyun
• 0
0
votes
0
replies
151
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
4 days ago by
Samantha
• 0
0
votes
1
reply
183
views
Microbial Signal Transduction Database
MiST
updated 4 days ago by
zx8754
11k • written 4 days ago by
Shravani
• 0
0
votes
1
reply
202
views
DESeq2 error
DESeq2
updated 5 days ago by
ATpoint
82k • written 5 days ago by
sooni
▴ 20
0
votes
0
replies
138
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
5 days ago by
singcell
• 0
0
votes
1
reply
208
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated 4 days ago by
ATpoint
82k • written 5 days ago by
Amr
▴ 160
0
votes
2
replies
220
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
4 days ago by
jain72744
▴ 10
1,000 results • Page
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Recent Votes
Comment: Bamutils/ClipOverlap
Comment: How to calculate coverage of Nanopore long read data?
Comment: Overlapping Ranges within Granges object
Answer: Difference between Genotype 0|1 and 1|0 in VCF file?
Answer: how to keep reads in a fasta file based on a seq id list in R?
Answer: The total expressed genes in RNA-Seq data
C: Re-arrange conditions in Seurat
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Comment: BWA alignment
by
a.alnawfal.1992
▴ 260
that's great, but i believe the issue is related to stdin rather than index
Comment: BWA alignment
by
a.alnawfal.1992
▴ 260
it is not!!
Comment: How to calculate coverage of Nanopore long read data?
by
Arton
• 0
Thank you! I eventually used the information generated by three tools (samtools coverage+ mosdepth + NanoPlot).
Comment: Alphaphold 3 pLDDT coloring scheme in chimerax?
by
mbrav005
• 0
Thank you Sir! you are right my model is not very good. Do You know how I can improve the scores. Also I am able to color the structure by …
Comment: Polish a large genome with Pilon
by
sansan_96
▴ 90
..........
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
you are on to something… if I use reduce to find the “overlaping regions” in a secon GRanges object, what do I do next?
Comment: Using ggplotly in R
by
jen
▴ 10
Thank you Jared for your response. I took a look at the documentation you provided and am trying my best to follow along, but can't seem to…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
by
Juke34
8.6k
Right I heard there is an issue since Perl v5.36. You may have better luck using conda. Or the best way is to use the container. Or downgra…
Answer: Alphaphold 3 pLDDT coloring scheme in chimerax?
by
Mensur Dlakic
★ 27k
pLDDT scores are stored in the so-called B-factor column in PDB files. Below the `File` ribbon select `Molecule Display` and click on `b-fa…
Comment: Genome Visualization Tools
by
dlera.lozano
▴ 10
Thank you so much
Answer: Doubt about the process of annotation, detection, identification and classificat
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Mensur Dlakic
★ 27k
Depends on the context. `TE detection` and `TE identification` could mean the same thing if they refer to presence/absence of TEs. `TE iden…
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr
by
Ram
43k
Please accept your own answer to mark the post as solved.
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Ram
43k
A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accep…
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Prawesh
• 0
thanks, it's working now.
Answer: Genome Visualization Tools
by
GenoMax
142k
@cmdcolin has a great list here: https://github.com/cmdcolin/awesome-genome-visualization
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