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372 results • Page
2 of 8
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Votes
Replies
0
votes
0
replies
75
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
1 day ago by
feather-W
• 0
2
votes
3
replies
171
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
updated 6 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
70
views
Annotating single cell data automatically
cell
annotation
single
1 day ago by
Gerard
• 0
0
votes
0
replies
74
views
News:
Online course: DNA methylation
Pacbio
Nanopore
DnaMethylation
Evolution
1 day ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
99
views
Job:
Ensembl Plants Senior Bioinformatician
ebi
embl
genomics
ensembl
1 day ago by
Ben_Ensembl
★ 2.4k
1
vote
3
replies
171
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
updated 1 hour ago by
ATpoint
81k • written 1 day ago by
HyperEvo
• 0
0
votes
1
reply
129
views
RNA-seq bacteria contamination
RNA-seq
updated 1 day ago by
GenoMax
141k • written 1 day ago by
sh
• 0
0
votes
2
replies
166
views
Result of running of p3_in.pl
primer3
updated 1 day ago by
GenoMax
141k • written 1 day ago by
nasri
• 0
0
votes
1
reply
115
views
FAM FILE
file
Fam
1 day ago by
Eleonora
• 0
0
votes
0
replies
64
views
Imputation advice
imputation
1 day ago by
kl
▴ 10
2
votes
5
replies
219
views
Per base sequence content error in RNAseq analysis
RNA-seq
analysis
updated 1 day ago by
GenoMax
141k • written 1 day ago by
ahmad.sajad4541
• 0
0
votes
0
replies
80
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
1 day ago by
Enrique
• 0
3
votes
5
replies
523
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
1 day ago by
n_navy
• 0
0
votes
0
replies
67
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
1 day ago by
sativus
▴ 20
6
votes
3
replies
153
views
Interpretting IGV output
IGV
updated 1 day ago by
Carlo Yague
8.7k • written 1 day ago by
analyst
▴ 20
0
votes
1
reply
160
views
homology modelling using swiss model
homology-modeling
swiss-model
updated 1 day ago by
colindaven
6.4k • written 2 days ago by
Ayush
• 0
0
votes
0
replies
69
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
1 day ago by
Biostars2200
• 0
1
vote
5
replies
229
views
DYH17 Structure Prediction
BLAST
Protein-Structure-Prediction
27 minutes ago by
anasjamshed
▴ 120
0
votes
0
replies
103
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 1 day ago by
Carlo Yague
8.7k • written 1 day ago by
Atul K.
• 0
3
votes
2
replies
242
views
p-value and Boneferroni adjusted p-value the same in R
Bonferroni
R
Statistics
p-value
Fisher
1 day ago by
kristiewyleung
• 0
1
vote
5
replies
397
views
Marking duplicates using UMIs
Deduplication
UMI
updated 1 day ago by
i.sudbery
19k • written 2 days ago by
Lipika
• 0
0
votes
0
replies
132
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 2 days ago by
Ram
43k • written 2 days ago by
sainavyav22
• 0
0
votes
0
replies
133
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
2 days ago by
rthapa
▴ 90
0
votes
0
replies
124
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
2 days ago by
Mamatha Y S
• 0
0
votes
0
replies
124
views
News:
upcoming online statistical courses
Statistics
R
Data-Analysis
updated 2 days ago by
Ram
43k • written 2 days ago by
carlopecoraro2
★ 2.5k
0
votes
4
replies
496
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq
gene-expression
updated 2 days ago by
ATpoint
81k • written 3 days ago by
rheab1230
▴ 140
0
votes
2
replies
241
views
bam merging for archaic samples
samtools
bam
updated 2 days ago by
Ram
43k • written 3 days ago by
Matteo Ungaro
▴ 100
7
votes
6
replies
419
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
2 days ago by
analyst
▴ 20
1
vote
1
reply
244
views
Removing Illumina microarray probes with no expression HumanHT-12v4
microarray
HumanHT-12v4
Illumina
updated 3 days ago by
Gordon Smyth
★ 7.0k • written 3 days ago by
Bioinformatician
• 0
1
vote
0
replies
523
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
3 days ago by
mathavanbioinfo
▴ 90
1
vote
1
reply
285
views
GTF file from Stringtie to R Studio for either Ballgown or DESeq2
Stringtie
Cufflinks
Ballgown
DESeq2
updated 3 days ago by
Ram
43k • written 3 days ago by
Nina
• 0
2
votes
5
replies
484
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis
MEGA
updated 2 days ago by
Mensur Dlakic
★ 27k • written 3 days ago by
Giorgio
• 0
2
votes
1
reply
274
views
Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
shotgun
metagenomics
blastp
taxonomy
updated 3 days ago by
GenoMax
141k • written 3 days ago by
rebecca.calvo
• 0
0
votes
0
replies
202
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
2 days ago by
abhishekghadge
• 0
2
votes
5
replies
658
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 2 days ago by
Jesse
▴ 740 • written 3 days ago by
Ann
★ 2.4k
0
votes
0
replies
180
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 3 days ago by
Ram
43k • written 3 days ago by
mja
• 0
0
votes
0
replies
183
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
3 days ago by
Nitin
• 0
1
vote
5
replies
530
views
Duplicate marking, read names, and the SRA
SRA
MarkDuplicates
updated 3 days ago by
GenoMax
141k • written 3 days ago by
Luka
• 0
0
votes
0
replies
182
views
absolute path for symbolic links in Snakefile
Snakemake
updated 3 days ago by
Ram
43k • written 3 days ago by
yifangt86
▴ 60
0
votes
0
replies
176
views
Chemical structure validation
structure
cap
validation
metabolite
3 days ago by
Rodolfo Adrián
• 0
3
votes
8
replies
1.2k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq
Cellranger
STARsolo
10X
updated 3 days ago by
swbarnes2
14k • written 9 months ago by
bp22
▴ 80
0
votes
1
reply
252
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 3 days ago by
GenoMax
141k • written 3 days ago by
bioyas
▴ 10
0
votes
0
replies
197
views
Copy number variation plot
Copy-number-variation
genomics
updated 4 days ago by
Ram
43k • written 4 days ago by
Emmi
• 0
1
vote
5
replies
678
views
RNA seq differential expression analysis
RNA-seq
normalization
updated 4 days ago by
BioinfGuru
★ 1.7k • written 5 days ago by
rrehimi
• 0
0
votes
0
replies
170
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
4 days ago by
DanielEB_fisk
▴ 20
0
votes
1
reply
271
views
Could you please assist in identifying this cluster?
single-cell
updated 4 days ago by
Ram
43k • written 4 days ago by
Kazo
• 0
4
votes
9
replies
2.6k
views
Tool:
CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.2 years ago by
dvelmeshev
• 0
2
votes
7
replies
5.2k
views
6 follow
Memory usage of picard Samsort
Picard
SortSam
updated 4 days ago by
ATpoint
81k • written 7.1 years ago by
boymin2020
▴ 80
5
votes
13
replies
1.0k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 3 days ago by
ATpoint
81k • written 4 days ago by
BioinfGuru
★ 1.7k
1
vote
1
reply
403
views
Plink merge errors.
cygwin64
bed
PLINK
4 days ago by
Dinmukhamed
• 0
372 results • Page
2 of 8
Recent Votes
Comment: Redirection of Duplicate PMIDs
Comment: Failed kmer content
Using vg gamsort with naive sorting algorithm
Answer: Using vg gamsort with naive sorting algorithm
Interested in Spatial Omics?
Interested in Spatial Omics?
Comment: Downsampling fastq file
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Recent Awards •
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Popular Question
to
Kash
▴ 110
Scholar
to
GenoMax
141k
Scholar
to
anovak
▴ 120
Popular Question
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pfee418
▴ 10
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sarahmanderni
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Recent Replies
Comment: Subset Seurat object from Xenium spatial data
by
bk11
★ 2.3k
For subsetting a sample, you can do something like this- Idents(seuratObj) <- "orig.ident" subj1 <- c("subject_1") subj1_seur…
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
Ok! I have a recommendation. I'll submit it as an answer, pending your feedback. vincent
Comment: DYH17 Structure Prediction
by
anasjamshed
▴ 120
In modeller we need to use templates as well.so 63% is acceptable
Comment: DYH17 Structure Prediction
by
Ram
43k
Mensur said > The latter option assumes you know how to use Modeller Do you know how to use Modeller? I vaguely recall there being a mini…
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
by
GenoMax
141k
OP is working with long reads so the chances of reads aligning to unlocalized scaffolds are relatively small. Doing some testing may be suf…
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
by
ATpoint
81k
I personally think that comparing the same peak between conditions is meaningful and comparing peaks within the same sample is not.
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
by
ATpoint
81k
These regions are present in the genome and removing them might incorrectly redirect alignments to known genes. I don't see why you would r…
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
by
njornet
▴ 20
Ok thank you! Do you know if there is an easy way of doing so with ncbi-genome-download or I need to use another tool?
Comment: Using vg gamsort with naive sorting algorithm
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: Redirection of Duplicate PMIDs
by
dominickd
• 0
The scope is all publications related to grants from an NIH award program. There are currently ~120k publications in total (about a few hun…
Answer: Using vg gamsort with naive sorting algorithm
by
anovak
▴ 120
The `-d` sorting mode does the entire sort in memory, so it will only work if you have enough memory to load your whole GAM file. To fin…
Comment: Redirection of Duplicate PMIDs
by
dominickd
• 0
I have a list of PMIDs for publications linked to a list of grants, exported from NIH RePORTER.
Comment: Plot DNA methylation level of DMR on the basis of certain genes
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
by
GenoMax
141k
Yes you can remove those if you are only interested in annotated genes.
Comment: Help for coding: Trinity for differential gene expression studies
by
mchour
• 0
[This could help][1] [1]: https://github.com/trinityrnaseq/RNASeq_Trinity_Tuxedo_Workshop/wiki/Trinity-De-novo-Transcriptome-Assembly-W…
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