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168 results • Page
2 of 4
Sort: replies
Rank
Views
Votes
Replies
1
vote
4
replies
329
views
Single cell analysis: Unable to subset cells in seurat object using desired nFeature_RNA cut off
single-cell
4 days ago by
sc_analysis
• 0
1
vote
4
replies
413
views
some error in building kraken2 database
metagenome
kraken2
updated 5 days ago by
GenoMax
142k • written 5 weeks ago by
Art1ess
• 0
3
votes
4
replies
6.3k
views
MAUVE: No gene annotations in Genbank file alignments
software-error
MAUVE
RAST
genbank
alignment
updated 6 days ago by
pramach1
▴ 40 • written 9.8 years ago by
tptacek3050
▴ 70
3
votes
4
replies
279
views
Search within posts based on tags using the Biostars API
api
meta
3 hours ago by
Bálint
▴ 10
5
votes
3
replies
5.9k
views
Attempt to set 'rownames' on an object with no dimensions
R
microbiome
spieceasi
updated 2 days ago by
GenoMax
142k • written 3.6 years ago by
ks.sholohova
▴ 30
0
votes
3
replies
385
views
Tool:
Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvages Failed Runs
NovaDemux
NovaSeq
Illumina
Demultiplexing
Barcode
4 days ago by
Brian Bushnell
20k
0
votes
3
replies
169
views
coding and non-coding region of the viral genome
viral-genome
updated 1 hour ago by
dthorbur
★ 2.0k • written 1 day ago by
Ghada
• 0
1
vote
3
replies
307
views
How to calculate cell type frequency between two groups in single cell data
Seurat
single-cell
sc-RNA
cell-type
updated 3 days ago by
Bastien Hervé
5.3k • written 4 days ago by
Sara
▴ 30
1
vote
3
replies
915
views
Which 1000 genomes 30x files should I use for imputation?
1000genomes
imputation
SNP
updated 6 days ago by
David-walson
• 0 • written 16 months ago by
Apprentice
▴ 160
2
votes
3
replies
2.2k
views
How to use pacbio reads to join contigs
assembly
tgs
pacbio
updated 3 hours ago by
Wyclif
• 0 • written 6.1 years ago by
934963534
▴ 20
7
votes
3
replies
13k
views
Z score in RNAseq
RNA-Seq
Zscore
updated 6 days ago by
Akash D
▴ 60 • written 6.5 years ago by
rob.costa1234
▴ 310
5
votes
3
replies
217
views
FastQC interpretation - 16S sequencing
interpretation
amplicon
Fastqc
16S
updated 6 days ago by
GenoMax
142k • written 6 days ago by
Christopher
▴ 10
3
votes
3
replies
191
views
How do i calculate the mean of triplicates in a data.frame based on pattern?
tidyverse
r
updated 51 minutes ago by
gglim
▴ 140 • written 1 day ago by
Assa Yeroslaviz
★ 1.9k
1
vote
3
replies
244
views
Trimmomatic running but files containing purged reads are empty
fastqc
fastq
trimmomatic
updated 6 days ago by
GenoMax
142k • written 6 days ago by
Wilber0x
▴ 50
1
vote
3
replies
304
views
Failed to download data from EBI with ascp
EBI
aspera
updated 1 day ago by
jude
• 0 • written 6 weeks ago by
biock
▴ 60
1
vote
3
replies
331
views
Error when looping over multiple columns in a data frame in R
Statistics
R
updated 5 days ago by
Jeremy
▴ 910 • written 6 days ago by
Mohamed Samir
▴ 30
0
votes
3
replies
404
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 5 days ago by
ATpoint
82k • written 5 days ago by
shahzaibali
• 0
1
vote
3
replies
214
views
downloading chemical database from ChEMBL
ChEMBL
PyRMD
Virtual-Screening
updated 6 days ago by
GenoMax
142k • written 7 days ago by
s
• 0
0
votes
3
replies
224
views
Splitting query fasta file for Diamond Blastp make the process faster?
DIAMOND
5 days ago by
kmat
• 0
2
votes
3
replies
274
views
How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tools
NucleotideDiversity
mtDNA
PacBio
5 days ago by
hashim.rana11
▴ 20
3
votes
3
replies
239
views
Unexpected read length from NGS
NGS
Illumina
5 days ago by
QX
• 0
2
votes
3
replies
320
views
How do we do quantification using stringtie merge option for all the merged samples generated.
stringtie
quantification
2 days ago by
Varsha
• 0
1
vote
2
replies
252
views
Setting a threshold on gene expression for subsetting (scRNA-seq)
scRNA-seq
updated 2 days ago by
LauferVA
4.2k • written 4 days ago by
carolofharvest
▴ 40
3
votes
2
replies
219
views
converting transcript IDs (Ensembl) to gene symbols in R
RNA-seq
updated 6 days ago by
GenoMax
142k • written 7 days ago by
ashkan
▴ 160
3
votes
2
replies
192
views
Multiplexing for pooled CRISPR screen sequencing
multiplex
CRISPR-screen
Illumina
6 days ago by
Tuấn Anh
• 0
3
votes
2
replies
187
views
How to interpret this plotMDS of three disease clusters?
microarray
plotMDS
DEGs
updated 5 days ago by
ATpoint
82k • written 6 days ago by
egascon
• 0
0
votes
2
replies
684
views
minfi::getQC - is default badsamplecutoff of 10.5 always appropriate? ~half of samples fail by this measure
getqc
ewas
minfi
updated 5 days ago by
June
• 0 • written 10 months ago by
rkb965
• 0
0
votes
2
replies
257
views
What do the transcript variant # mean in RefSeq?
refseq
updated 5 days ago by
Ram
44k • written 5 days ago by
curious
▴ 750
0
votes
2
replies
192
views
CreateSeuratObject taking very long
seurat
5 days ago by
eae6d2e7
• 0
1
vote
2
replies
251
views
Construction of circos plot from WGS data
WGS
Circos
5 days ago by
Anitha
▴ 10
1
vote
2
replies
288
views
Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
PLINK
GWAS
SNP
4 days ago by
F110152169
• 0
1
vote
2
replies
322
views
Error when i use EVidenceModeler to do the genome annotation
EVidenceModeler
annotation
genome
3 days ago by
peanut
• 0
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 2 days ago by
Asaf
10k • written 6.3 years ago by
m.koohi.m
▴ 120
0
votes
2
replies
241
views
perl Error - needLargeMem Bigwig
Bigwig
perl
mitosalt
1 day ago by
marco.barr
▴ 130
0
votes
2
replies
150
views
identify the coordinate for coding and non_coding region.
coding
non_coding
1 day ago by
Ghada
• 0
4
votes
2
replies
253
views
Number of non-ATCG nucleotides replaced by Salmon
rna-seq
stringtie
salmon
updated 1 day ago by
Ram
44k • written 4 days ago by
Tonya S.
▴ 10
2
votes
2
replies
359
views
Annotating single cell data automatically
single-cell
updated 1 day ago by
Nat.Nataren
▴ 30 • written 5 weeks ago by
Gerard
• 0
3
votes
2
replies
213
views
vg autoindex seems stuck after a week of running
vg
pangenome
1 day ago by
StevieP
▴ 10
1
vote
2
replies
204
views
Salmon vs Kallisto vs RSEM
RSEM
quantification
kallisto
Salmon
1 day ago by
Mohamed Abderrahmane
▴ 20
2
votes
2
replies
230
views
Help me with Heatmap
RNA-seq
R
DESeq2
updated 1 day ago by
zx8754
11k • written 1 day ago by
vmpsb
• 0
0
votes
2
replies
172
views
Salmon ~ Effective Length
Salmon
updated 22 hours ago by
GenoMax
142k • written 1 day ago by
chrisk
• 0
1
vote
2
replies
175
views
Polygenic Risk Score calculation
snp
polygene
prs
variants
22 hours ago by
ashaneev07
▴ 20
2
votes
2
replies
137
views
dbNSFP4.7a database format to Annovar Format?
snp
annovar
NGS
dbNSFP
updated 19 hours ago by
Ram
44k • written 1 day ago by
Clark_BioMorgan
▴ 50
1
vote
2
replies
149
views
How do I check if a DNA sequence of a gene is supported by RNAseq data?
Genetics
RNA-seq
Phase-variation
Alignment
18 hours ago by
Jack
• 0
0
votes
2
replies
270
views
Tools for chromosomal aneuploidy detection
human-genetics
aneuploidy
NGS
updated 15 hours ago by
Ram
44k • written 5 days ago by
adarsh_pp
▴ 40
0
votes
2
replies
247
views
How to decrease the motif score?
Motif-score
updated 14 hours ago by
Ram
44k • written 3 days ago by
Hadia
• 0
0
votes
2
replies
230
views
Mutation counts corrected by number of samples
mutations
WES
genomics
WGS
13 hours ago by
garcesj
▴ 50
1
vote
2
replies
215
views
How to Convert CNV Data to CNA Format for Reproducing Results with the Padma Package?
multi-omics
CNV
R
12 hours ago by
Ngrin
• 0
4
votes
2
replies
184
views
when I use htslib to write a bam. Error of "truncated file" shows by samtools
bam
htslib
7 hours ago by
Aaron
▴ 10
0
votes
2
replies
911
views
Manual Polygenic Risk Score calculation
calculation
steps
PRS
updated 2 hours ago by
ashaneev07
▴ 20 • written 16 months ago by
Roy
▴ 10
168 results • Page
2 of 4
Recent Votes
Answer: RNA-Seq analysis
Comment: UMI-Tools knee-method has great influence on the results of white list
Answer: RNA-Seq analysis
Answer: salmon with long read
I cannot download VG in any way
Comment: I cannot download VG in any way
A: Bam File: Change Chromosome Notation
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Recent Replies
Comment: bcl-convert cannot create output directory structure at the path specified
by
marco.barr
▴ 130
I've never received this error before.. but you could try checking the permissions
Answer: How do i calculate the mean of triplicates in a data.frame based on pattern?
by
gglim
▴ 140
``` library(dplyr) df %>% rowwise() %>% mutate(p767.AM = mean(c_across(contains("AM")))) ``` Maybe this is what you're looking for?
Answer: RNA-Seq analysis
by
Michael
54k
I think the situation you are finding yourself in is quite common. On a general note, as you are at the beginning of your PhD program, you …
Answer: RNA-Seq analysis
by
Nat.Nataren
▴ 30
We'll need a lot more information to help, you haven't given us much to work with. What organism are you working in? What is the experi…
Comment: Cut&Run and heatmap
by
gglim
▴ 140
I'll take a look at these peaks in IGV with the signal files and set a threshold for filtering.
Comment: NCBI vs Ensembl - Ortholog genes Information
by
José
▴ 10
Thanks for the answer and the advice.
Comment: NCBI vs Ensembl - Ortholog genes Information
by
José
▴ 10
Thak you so much for your answer and advice.
Comment: coding and non-coding region of the viral genome
by
dthorbur
★ 2.0k
You also have intronic regions between exons that also count as non-coding regions. Psuedogenes and non-coding RNAs too. I'm sure there are…
Comment: samsift can't find the AS tag to filter a bam file generated using bowtie2
by
Pierre Lindenbaum
162k
what is AS ? an attribute in a SAM record? Are you sure this is the way to access an attribute : `-f 'AS>94'` . Otherwise, just use `samt…
Comment: Filtering reads that map to both references
by
Pierre Lindenbaum
162k
see related : https://www.biostars.org/p/274183/
Comment: I cannot download VG in any way
by
dariober
14k
Downloading the binary as GenoMax (and the vgteam) suggests is most likely the best option. For the record, `git clone --recursive https://…
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2
by
Sara
▴ 30
It was 10X data, and I processed it using Seurat. Then, I came to the point of Pseudobulk using DESeq2. Does this mean I have to check whi…
Comment: UMI-Tools knee-method has great influence on the results of white list
by
i.sudbery
19k
We recommend alecin where it supports the kit you are using. As far as I'm aware it doesn't support custom read geometry yet, but does supp…
Answer: NCBI vs Ensembl - Ortholog genes Information
by
b.contreras.moreira
▴ 200
Hi José, orthology inference is tricky and that's why the <https://questfororthologs.org> consortium has been comparing **graph-based** an…
Comment: Manual Polygenic Risk Score calculation
by
ashaneev07
▴ 20
Hello, Did you calculate the score successfully? I'm also facing issues with prs score calculation.
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