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178 results • Page
2 of 4
Sort: Views
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Views
Votes
Replies
1
vote
4
replies
319
views
How to find SRA sequences of some fungal whole genome sequences if only Biosample ID is available?
SRA
whole-genome-sequencing
NCBI
updated 5 days ago by
Ram
44k • written 6 days ago by
Harshita
• 0
2
votes
6
replies
314
views
How to get the ratio of allele counts from GATK derived VCF file?
Freebayes
GATK
SNP
VCF
3 days ago by
anikcropscience
▴ 230
2
votes
5
replies
311
views
Harmony integration group.by.var parameter
single-cell
harmony
6 hours ago by
Picasa
▴ 640
0
votes
3
replies
311
views
Tool:
Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvages Failed Runs
NovaDemux
NovaSeq
Illumina
Demultiplexing
Barcode
1 day ago by
Brian Bushnell
20k
1
vote
3
replies
310
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
4 days ago by
Pegasus
▴ 100
0
votes
3
replies
305
views
Kraken2 Custom Database non-deterministic results
Metagenomics
kraken2
updated 4 days ago by
colindaven
6.4k • written 6 days ago by
Bjorn
• 0
1
vote
2
replies
305
views
Error when i use EVidenceModeler to do the genome annotation
EVidenceModeler
annotation
genome
1 day ago by
peanut
• 0
1
vote
3
replies
300
views
Error when looping over multiple columns in a data frame in R
Statistics
R
updated 2 days ago by
Jeremy
▴ 910 • written 3 days ago by
Mohamed Samir
▴ 30
2
votes
5
replies
299
views
Z score
Z-score
updated 3 days ago by
Ram
44k • written 3 days ago by
Akash D
▴ 60
1
vote
5
replies
299
views
How to scrape BioMart data from https://sorfs.ugent.be/ website
BioMart
updated 6 hours ago by
Pierre Lindenbaum
162k • written 2 days ago by
QX
• 0
0
votes
2
replies
288
views
How can I calculate the OS of each patient?
overall-survival
6 days ago by
Pedro
• 0
1
vote
4
replies
285
views
Single cell analysis: Unable to subset cells in seurat object using desired nFeature_RNA cut off
single-cell
2 days ago by
sc_analysis
• 0
1
vote
4
replies
284
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
4 days ago by
shpak.max
▴ 50
0
votes
6
replies
282
views
from CRAM to fastq
FASTQ
WGS
CRAM
updated 3 days ago by
ATpoint
82k • written 4 days ago by
machaalani29
• 0
2
votes
4
replies
274
views
Allele count of 2 for homoplasmic MT variants in VCF
Variant-Calling
GATK
VCF
3 days ago by
Arton
▴ 10
0
votes
4
replies
269
views
GO analysis: p-value range
GO
R
updated 6 days ago by
Matthias Zepper
4.6k • written 6 days ago by
sooni
▴ 20
0
votes
1
reply
266
views
GWAS Phenotypes
GWAS
updated 3 days ago by
韩雨
• 0 • written 5 weeks ago by
solomoncharles77
▴ 90
0
votes
3
replies
266
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 5 days ago by
marco.barr
▴ 130 • written 6 days ago by
Mohamed Samir
▴ 30
1
vote
3
replies
260
views
seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from input file
subseq
seqtk
extractionproblem
updated 6 days ago by
GenoMax
142k • written 7 days ago by
KHURRAM SHAHZAD
• 0
1
vote
2
replies
252
views
Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
PLINK
GWAS
SNP
2 days ago by
F110152169
• 0
0
votes
3
replies
251
views
z-score of gene set
z-score
scRNA
gene-set
4 days ago by
Hien
• 0
2
votes
4
replies
250
views
Filter Genome for Specific Sites
bedtools
updated 5 days ago by
Ram
44k • written 6 days ago by
Anita
• 0
0
votes
5
replies
249
views
Why most genes have high padj values
RNA-seq
DEG
updated 6 days ago by
Ram
44k • written 6 days ago by
mnx0723
• 0
0
votes
4
replies
247
views
Where to find old version of GATK best practice
gatk
5 days ago by
Zhenyu Zhang
★ 1.2k
1
vote
3
replies
244
views
How to calculate cell type frequency between two groups in single cell data
Seurat
single-cell
sc-RNA
cell-type
updated 1 day ago by
Bastien Hervé
5.3k • written 2 days ago by
Sara
▴ 30
1
vote
2
replies
244
views
News:
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
BestTalk
PlatformPresentation
offtopic
updated 5 days ago by
colindaven
6.4k • written 6 days ago by
Dr.
• 0
0
votes
4
replies
243
views
Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
GATK
UnifiedGenotyper
4 days ago by
shpak.max
▴ 50
1
vote
2
replies
239
views
Construction of circos plot from WGS data
WGS
Circos
2 days ago by
Anitha
▴ 10
0
votes
2
replies
235
views
How do we do quantification using stringtie merge option for all the merged samples generated.
stringtie
quantification
updated 3 days ago by
i.sudbery
19k • written 4 days ago by
Varsha
• 0
2
votes
3
replies
233
views
How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tools
NucleotideDiversity
mtDNA
PacBio
2 days ago by
hashim.rana11
▴ 20
1
vote
3
replies
233
views
Trimmomatic running but files containing purged reads are empty
fastqc
fastq
trimmomatic
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Wilber0x
▴ 50
0
votes
2
replies
230
views
What do the transcript variant # mean in RefSeq?
refseq
updated 2 days ago by
Ram
44k • written 3 days ago by
curious
▴ 750
0
votes
0
replies
227
views
ERROR with Maker annotation: The assumed RepeatMasker installation directory /opt/home/sony/miniconda3/envs/MAKER2/share/RepeatMasker does not ap…
RepeatMasker.
MAKER.
annotation.
1 day ago by
Sony
▴ 10
3
votes
3
replies
226
views
Unexpected read length from NGS
NGS
Illumina
2 days ago by
QX
• 0
0
votes
1
reply
223
views
Annotating single cell data automatically
single-cell
updated 2 days ago by
Ram
44k • written 4 weeks ago by
Gerard
• 0
0
votes
5
replies
222
views
Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
Bowtie
2 days ago by
Deepthi
• 0
0
votes
4
replies
221
views
merge overlaps and remove non overlap genomic windows
BED
intersection
overlap
3 days ago by
reza
▴ 300
0
votes
3
replies
219
views
GATK Structural Variants Pipeline - Steps
SV
GATK
Variant-Calling
updated 6 days ago by
Ram
44k • written 6 days ago by
Bioinformatics_begginner
▴ 20
0
votes
2
replies
218
views
How to generate an Upset plot in R to plot the shared variants between cell free DNA samples
r
Upset
6 days ago by
sainavyav22
• 0
1
vote
2
replies
217
views
Elbow plot question (scRNA seq data analysis - scanpy tutorial)
scanpy
5 days ago by
ojaswinipandey
• 0
0
votes
3
replies
216
views
Splitting query fasta file for Diamond Blastp make the process faster?
DIAMOND
2 days ago by
kmat
• 0
3
votes
2
replies
215
views
converting transcript IDs (Ensembl) to gene symbols in R
RNA-seq
updated 4 days ago by
GenoMax
142k • written 5 days ago by
ashkan
▴ 160
0
votes
2
replies
213
views
Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis of Spleen Samples from Different Conditions
Seurat
scRNA-Seq
Single-Cell
5 days ago by
Shukai
• 0
5
votes
3
replies
209
views
FastQC interpretation - 16S sequencing
interpretation
amplicon
Fastqc
16S
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Christopher
▴ 10
1
vote
3
replies
207
views
Question about samtools view flags (paired reads vs. properly paired reads)
samtools
updated 4 days ago by
Pierre Lindenbaum
162k • written 5 days ago by
mrk
• 0
4
votes
1
reply
205
views
PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while adj p < 0.05 does not.
RNA-seq
padj
p-value
updated 2 days ago by
swbarnes2
14k • written 3 days ago by
May Ling
• 0
1
vote
3
replies
203
views
downloading chemical database from ChEMBL
ChEMBL
PyRMD
Virtual-Screening
updated 4 days ago by
GenoMax
142k • written 4 days ago by
s
• 0
1
vote
2
replies
200
views
How to find identical sequences in genome fasta file (by Python or any possible program) ?
fasta
updated 6 days ago by
Ram
44k • written 6 days ago by
Sony
▴ 10
0
votes
2
replies
194
views
vcf phasing
beagle
WhatsHap
phasing
4 days ago by
safeassli
▴ 10
2
votes
0
replies
194
views
Job:
Permanent Position as Researcher/Computational Biologist at the National Genomics Infrastructure (Sweden)
Genomics
Sequencing
Sweden
Stockholm
SciLifeLab
3 days ago by
Matthias Zepper
4.6k
178 results • Page
2 of 4
Recent Votes
Answer: How to scrape BioMart data from https://sorfs.ugent.be/ website
Low DESeq2 Sensivity on scRNA Pseudobulk Samples
DESEQ2: How can I convert ensembl gene id's to HGNC gene names.
Problem with Ensembl version identifiers after running DESeq2
Issues with adding gene name and entrez ID to DESeq2 result having Ensembl ID.
A: Looking for differential gene expression between treatment, within a specific cl
How to compare cell-type ratios in sc-RNA seq data?
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Comment: Setting a threshold on gene expression for subsetting (scRNA-seq)
by
LauferVA
4.2k
Generally, I cannot advise this in the abstract. The thing is, depending on the treatment group and so forth, there are some transcripts th…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
44k
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: Getting differential ChIP-seq peaks between conditions after calling consensus p
by
Alexandra
• 0
Thank you for your response! Interesting paper.
Comment: How to scrape BioMart data from https://sorfs.ugent.be/ website
by
Pierre Lindenbaum
162k
> 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: Harmony integration group.by.var parameter
by
Picasa
▴ 640
@jaredandrews07 If I integrate using Donor: ```R RunHarmony(seu_obj, group.by.vars = c("Donor_ID")) ``` Should I also normalize my data…
Comment: How to scrape BioMart data from https://sorfs.ugent.be/ website
by
QX
• 0
thank you so much!
Comment: Attempt to set 'rownames' on an object with no dimensions
by
elbakri.fatimazahrae
• 0
hello everyone, I got the same error for a function immuCellAI_new; result <- ImmuCellAI_new(countData = expr_data_log22, data_type =…
Comment: Merging multiple samples in Seurat
by
Picasa
▴ 640
did you split by sample or donor ?
Comment: Harmony integration group.by.var parameter
by
Picasa
▴ 640
For downstream analysis, after integration, my plan is to annotate each cluster/cell type and then perform a DGE analysis of KO versus WT f…
Comment: How to calculate cell type frequency between two groups in single cell data
by
Bastien Hervé
5.3k
That is correct
Comment: Setting a threshold on gene expression for subsetting (scRNA-seq)
by
ATpoint
82k
That depends on the data and the marker. Generally I would plot violins per cluster for the marker(s) and see whether one robustly overexpr…
Comment: Error when i use EVidenceModeler to do the genome annotation
by
peanut
• 0
thank you so much ,i get it
Comment: Number of non-ATCG nucleotides replaced by Salmon
by
Tonya S.
▴ 10
Oops, yes, that must be where they are coming from. For some reason, I was thinking the genome was just soft-masked. How embarrassing! Than…
Answer: Number of non-ATCG nucleotides replaced by Salmon
by
Rob
6.6k
If there are no other signs that anything is awry, I probably wouldn't worry about this. Is it possible that these non-canonical nucleotid…
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage
by
Brian Bushnell
20k
I examined nine 10B runs and five 25B runs (we just started getting 25B flowcells a few months ago). I did not pay close attention but it …
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