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173 results • Page
2 of 4
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2
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4
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1.0k
views
samtools mpileup error - 1 samples in 1 input files
samtools
BAM
mpileup
SAM
updated 1 hour ago by
Damla
• 0 • written 2.4 years ago by
joseph.kelly.94
▴ 10
0
votes
3
replies
365
views
What is a good way to do gene differentials in single cell data where one group is small 90 cells and the other group 30,000 cells or 2000 cells.
cell
RNA-Seq
single
updated 3 days ago by
ATpoint
82k • written 4 days ago by
shahzaibali
• 0
0
votes
3
replies
217
views
Splitting query fasta file for Diamond Blastp make the process faster?
DIAMOND
3 days ago by
kmat
• 0
2
votes
3
replies
261
views
How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tools
NucleotideDiversity
mtDNA
PacBio
3 days ago by
hashim.rana11
▴ 20
3
votes
3
replies
230
views
Unexpected read length from NGS
NGS
Illumina
3 days ago by
QX
• 0
1
vote
3
replies
284
views
How to calculate cell type frequency between two groups in single cell data
Seurat
single-cell
sc-RNA
cell-type
updated 2 days ago by
Bastien Hervé
5.3k • written 3 days ago by
Sara
▴ 30
1
vote
3
replies
325
views
Filtering VCF files based on VAF giving incorrect results
GATK
picard
VCF
bcftools
updated 6 days ago by
Ram
44k • written 12 days ago by
Arton
▴ 10
0
votes
3
replies
182
views
Generating a Bed file from a Fasta file
bed
NullSeq
updated 6 days ago by
Ram
44k • written 6 days ago by
pirku
• 0
0
votes
3
replies
356
views
Tool:
Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvages Failed Runs
NovaDemux
NovaSeq
Illumina
Demultiplexing
Barcode
2 days ago by
Brian Bushnell
20k
0
votes
3
replies
1.8k
views
Running STRUCTURE from command line
STRUCTURE
updated 6 days ago by
Ram
44k • written 3.0 years ago by
giulia.trauzzi
▴ 10
0
votes
3
replies
195
views
Where are the illumina adapters on Trimmomatic take from?
rna-seq
trimmomatic
updated 6 days ago by
GenoMax
142k • written 6 days ago by
bioinfo
▴ 150
1
vote
3
replies
211
views
Question about samtools view flags (paired reads vs. properly paired reads)
samtools
updated 6 days ago by
Pierre Lindenbaum
162k • written 6 days ago by
mrk
• 0
0
votes
3
replies
254
views
z-score of gene set
z-score
scRNA
gene-set
5 days ago by
Hien
• 0
0
votes
3
replies
306
views
Kraken2 Custom Database non-deterministic results
Metagenomics
kraken2
updated 5 days ago by
colindaven
6.4k • written 7 days ago by
Bjorn
• 0
1
vote
3
replies
209
views
downloading chemical database from ChEMBL
ChEMBL
PyRMD
Virtual-Screening
updated 5 days ago by
GenoMax
142k • written 6 days ago by
s
• 0
5
votes
3
replies
214
views
FastQC interpretation - 16S sequencing
interpretation
amplicon
Fastqc
16S
updated 5 days ago by
GenoMax
142k • written 5 days ago by
Christopher
▴ 10
1
vote
3
replies
239
views
Trimmomatic running but files containing purged reads are empty
fastqc
fastq
trimmomatic
updated 5 days ago by
GenoMax
142k • written 5 days ago by
Wilber0x
▴ 50
0
votes
3
replies
237
views
How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat
Pseudobulk
single-cell
DESeq2
scRNA
updated 7 hours ago by
ATpoint
82k • written 2 days ago by
Sara
▴ 30
2
votes
3
replies
309
views
How do we do quantification using stringtie merge option for all the merged samples generated.
stringtie
quantification
10 hours ago by
Varsha
• 0
2
votes
3
replies
764
views
Cut&Run and heatmap
and
bowtie2
MACS2
updated 49 minutes ago by
sogand
• 0 • written 13 months ago by
qudrat.nii
▴ 10
0
votes
3
replies
266
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 6 days ago by
marco.barr
▴ 130 • written 7 days ago by
Mohamed Samir
▴ 30
1
vote
3
replies
912
views
Which 1000 genomes 30x files should I use for imputation?
1000genomes
imputation
SNP
updated 4 days ago by
David-walson
• 0 • written 16 months ago by
Apprentice
▴ 160
7
votes
3
replies
13k
views
Z score in RNAseq
RNA-Seq
Zscore
updated 4 days ago by
Akash D
▴ 60 • written 6.5 years ago by
rob.costa1234
▴ 310
1
vote
3
replies
572
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 6 days ago by
Klaus S
▴ 160 • written 6 weeks ago by
Zeng Hao
▴ 40
5
votes
3
replies
5.8k
views
Attempt to set 'rownames' on an object with no dimensions
R
microbiome
spieceasi
updated 1 day ago by
GenoMax
142k • written 3.6 years ago by
ks.sholohova
▴ 30
1
vote
3
replies
322
views
Error when looping over multiple columns in a data frame in R
Statistics
R
updated 3 days ago by
Jeremy
▴ 910 • written 4 days ago by
Mohamed Samir
▴ 30
1
vote
2
replies
3.8k
views
How can run cd-hit-est with a clstr threshold less than 0.8?
cd-hit
cluster
updated 11 hours ago by
Asaf
10k • written 6.3 years ago by
m.koohi.m
▴ 120
0
votes
2
replies
215
views
perl Error - needLargeMem Bigwig
Bigwig
perl
mitosalt
9 hours ago by
marco.barr
▴ 130
3
votes
2
replies
191
views
Multiplexing for pooled CRISPR screen sequencing
multiplex
CRISPR-screen
Illumina
5 days ago by
Tuấn Anh
• 0
3
votes
2
replies
181
views
How to interpret this plotMDS of three disease clusters?
microarray
plotMDS
DEGs
updated 4 days ago by
ATpoint
82k • written 4 days ago by
egascon
• 0
2
votes
2
replies
96
views
How do i calculate the mean of triplicates in a data.frame based on pattern?
tidyverse
r
mean
summarize
updated 6 hours ago by
dariober
14k • written 7 hours ago by
Assa Yeroslaviz
★ 1.9k
3
votes
2
replies
218
views
converting transcript IDs (Ensembl) to gene symbols in R
RNA-seq
updated 5 days ago by
GenoMax
142k • written 6 days ago by
ashkan
▴ 160
1
vote
2
replies
218
views
Elbow plot question (scRNA seq data analysis - scanpy tutorial)
scanpy
6 days ago by
ojaswinipandey
• 0
0
votes
2
replies
196
views
vcf phasing
beagle
WhatsHap
phasing
5 days ago by
safeassli
▴ 10
0
votes
2
replies
435
views
transanno liftvcf "Error: length of chromosome [chr] is not equal to length in chain file. Are you using correct reference?"
liftover
transanno
5 days ago by
ezz3
• 0
0
votes
2
replies
680
views
minfi::getQC - is default badsamplecutoff of 10.5 always appropriate? ~half of samples fail by this measure
getqc
ewas
minfi
updated 4 days ago by
June
• 0 • written 10 months ago by
rkb965
• 0
1
vote
2
replies
247
views
News:
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
BestTalk
PlatformPresentation
offtopic
updated 6 days ago by
colindaven
6.4k • written 7 days ago by
Dr.
• 0
0
votes
2
replies
62
views
identify the coordinate for coding and non_coding region.
coding
non_coding
3 hours ago by
Ghada
• 0
1
vote
2
replies
242
views
Construction of circos plot from WGS data
WGS
Circos
3 days ago by
Anitha
▴ 10
4
votes
2
replies
222
views
Number of non-ATCG nucleotides replaced by Salmon
rna-seq
stringtie
indexing
salmon
updated 2 days ago by
Rob
6.6k • written 2 days ago by
Tonya S.
▴ 10
1
vote
2
replies
315
views
Error when i use EVidenceModeler to do the genome annotation
EVidenceModeler
annotation
genome
2 days ago by
peanut
• 0
0
votes
2
replies
117
views
Help me with Heatmap
RNA
R
seq
DESeq2
updated 2 hours ago by
MolGeek
▴ 50 • written 6 hours ago by
vmpsb
• 0
0
votes
2
replies
248
views
What do the transcript variant # mean in RefSeq?
refseq
updated 4 days ago by
Ram
44k • written 4 days ago by
curious
▴ 750
1
vote
2
replies
396
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 6 days ago by
finch
• 0 • written 3 months ago by
star
▴ 10
1
vote
2
replies
280
views
Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
PLINK
GWAS
SNP
3 days ago by
F110152169
• 0
1
vote
2
replies
213
views
Setting a threshold on gene expression for subsetting (scRNA-seq)
scRNA-seq
updated 1 day ago by
LauferVA
4.2k • written 2 days ago by
carolofharvest
▴ 40
0
votes
2
replies
217
views
Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis of Spleen Samples from Different Conditions
Seurat
scRNA-Seq
Single-Cell
6 days ago by
Shukai
• 0
1
vote
2
replies
195
views
How can we convert a vcf to fasta, so that I can blast some genes against that whole genome sequences?
blast
fasta
vcf
gene
updated 6 days ago by
Ram
44k • written 6 days ago by
Harshita
• 0
1
vote
2
replies
258
views
Failed to download data from EBI with ascp
EBI
aspera
updated 14 hours ago by
孝中
• 0 • written 6 weeks ago by
biock
▴ 60
0
votes
2
replies
211
views
Tools for chromosomal aneuploidy detection
genetics
aneuploidy
NGS
human
updated 11 hours ago by
a.alnawfal.1992
▴ 260 • written 4 days ago by
adarsh_pp
▴ 40
173 results • Page
2 of 4
Recent Votes
Comment: Functional enrichment analysis for unique gene IDs
Answer: How do i calculate the mean of triplicates in a data.frame based on pattern?
How do i calculate the mean of triplicates in a data.frame based on pattern?
C: snpEff assigned all variants as modifier intergenic
A: Problem in indexing toplevel genome with HISAT2
C: The Biostar Handbook. A bioinformatics e-book for beginners.
Answer: Error with BiocParallel. No barcodes files found
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Comment: Venter Genome Vcf
by
Jeremy Leipzig
22k
there are some violations in this VCF: - Invalid count number, with fixed count the number should be 1 or higher: key=INFO name=TSA type=St…
Answer: Cut&Run and heatmap
by
sogand
• 0
Hi all, I am new to cut&run or any peak-related analysis and appreciate any guidance on my issue here: I have analyzed peakcalling .txt …
Comment: Functional enrichment analysis for unique gene IDs
by
Pegasus
▴ 100
Since the locus-tags are unclassified, I used the CDS instead of the locus-tags to retrive their ensembl IDs using ensembl bacteria website…
Comment: samtools mpileup error - 1 samples in 1 input files
by
Damla
• 0
Could you find a solution to your problem?
Comment: txt file to bigwig
by
sogand
• 0
Hi all, I am new to these kind of analysis and appreciate any guidance on my issue here: I have analyzed peakcalling .txt files that are r…
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by
MolGeek
▴ 50
Hello! So, what is the correct design ? You will have to ask yourself, what do you want to compare? WT vs mut? If so it will be strain. 2…
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swbarnes2
14k
1) you have to say what question you are actually asking. There are few different designs that would address different questions. 2) work…
Comment: identify the coordinate for coding and non_coding region.
by
Ghada
• 0
mmmm I am not sure. This is how I generate my consnsus sequence # Get consensus fastq file samtools mpileup -uf KT992094.1.fasta…
Comment: identify the coordinate for coding and non_coding region.
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GenoMax
142k
Why do you have those N's at the beginning of the sequence? If the remainder of the sequence matches 100% then the initial N's may be wrong…
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by
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6.6k
It's nice that you've gone ahead and done some analysis of these results and their differences on your data yourself. These more general qu…
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
Mike Smith
★ 2.0k
In this location there is an "entrez" file which maps ensembl IDs to Entrez. It's probably as definitive as you're going to find: https://…
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
Anya
• 0
Tried it just recently with almost the same results. 456 out of 496 IDs for protein-coding genes returned as "NA" even though I can see NCB…
Answer: Download All The Bacterial Genomes From Ncbi
by
2284046470
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wget https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt awk -F '\t' '{if($12=="Complete Genome" && $11=…
Answer: How do i calculate the mean of triplicates in a data.frame based on pattern?
by
dariober
14k
I'm a happy user of [data.table](https://rdatatable.gitlab.io/data.table/): ``` library(data.table) dat <- structure(list(sgrna = c("Cont…
Comment: How do i calculate the mean of triplicates in a data.frame based on pattern?
by
Assa Yeroslaviz
★ 1.9k
I know it can be done with something like that: ``` cbind(p767.AM = (rowMeans(p767[,2:4])), p767.MM = (rowMeans(p767[,5:7]…
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