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775 results • Page
3 of 16
Sort: replies
Rank
Views
Votes
Replies
0
votes
7
replies
472
views
Highly inflated p-values in GWAS by regenie
regenie
plink
gwas
1 day ago by
cwwong13
▴ 20
2
votes
7
replies
681
views
VG mapping paired-end reads: error [xg]: multiple hits for XXX
variation-graph
reads
pangenome
vg
paired-end
22 days ago by
nkls063408
• 0
4
votes
7
replies
583
views
Help with Error: None of the requested features were found: PECAM1 in slot data
seurat
multiome
26 days ago by
Chris
▴ 180
0
votes
7
replies
2.7k
views
qPCR: Huge variation in fold change of genes between biological replicates
qpcr
fold-change
updated 10 days ago by
Ram
40k • written 5.3 years ago by
AP
▴ 80
3
votes
7
replies
259
views
Should I Learn Docker to Run Command Line Bioinformatics Tool?
Docker
updated 10 hours ago by
Yogi
▴ 10 • written 17 hours ago by
arriyaz.nstu
▴ 30
8
votes
7
replies
3.9k
views
Problem in indexing toplevel genome with HISAT2
RNA-Seq
genome
hisat2
hisat2-build
index
updated 26 days ago by
Apex92
▴ 270 • written 4.6 years ago by
Batu
▴ 240
0
votes
7
replies
592
views
What is wrong with my NCBI esearch command for 16S rRNA?
16S
NCBI
Entrez
assembly
updated 10 days ago by
GenoMax
134k • written 12 days ago by
Morgan S.
▴ 80
5
votes
7
replies
547
views
Can one sample t.test be used to determine statistical significance for log2FC values?
log2FC
T.test
updated 26 days ago by
dsull
★ 4.7k • written 27 days ago by
aUser
▴ 30
2
votes
7
replies
4.0k
views
GERP++ (gerpcol) error on a test data
GERP
updated 5 days ago by
Diana
• 0 • written 7.1 years ago by
kirill1984
▴ 10
2
votes
7
replies
2.6k
views
CWL: Getting output file of a CommandLineTool using glob
Common-Workflow-Language
cwl
updated 14 days ago by
Ram
40k • written 5.2 years ago by
skanwal
▴ 50
8
votes
7
replies
1.2k
views
Whole genome species clustering
phylogeny
assembly
phylogenetics
updated 27 days ago by
pmiller
• 0 • written 2.4 years ago by
robert.murphy
▴ 80
4
votes
7
replies
724
views
How to subtract a number from protein IDs?
blast
updated 4 days ago by
Ram
40k • written 3.1 years ago by
A_heath
▴ 140
5
votes
7
replies
413
views
Salmon index not progressing
salmon
updated 3 days ago by
Michael
53k • written 4 days ago by
camillab.
▴ 130
9
votes
7
replies
6.7k
views
Gc Content From Bam
gc
bam
awk
perl
updated 24 days ago by
Ram
40k • written 9.6 years ago by
filipzembol
▴ 170
3
votes
7
replies
601
views
GATK AnnotateVcfWithBamDepth returns zero DP for all variants in VCF
GATK
AnnotateVcfWithBamDepth
27 days ago by
ClkElf
▴ 50
0
votes
6
replies
872
views
FACS (Fluorescence-activated cell sorting NOT cyTOF),Automating the removal of dead and duplicated cells
FACS
4 days ago by
ccbb7aab4
▴ 20
4
votes
6
replies
2.6k
views
IDT vs primer 3 - PCR dimerisation
PCR
primer3
IDT
primer
updated 11 days ago by
Emrah
• 0 • written 3.1 years ago by
timothy.kirkwood
▴ 130
3
votes
6
replies
705
views
6 follow
Forum:
Is Bioinformatics a Professional Degree?
career
degree
26 days ago by
anasjamshed
▴ 120
7
votes
6
replies
526
views
Best practices scRNA-seq guide for beginer
scRNA-seq
eBook
24 days ago by
octpus616
▴ 80
3
votes
6
replies
465
views
summarize consecutive columns over a data frame
tidyverse
r
offtopic
updated 3 days ago by
Ram
40k • written 15 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
6
replies
544
views
How to get top 10 genes expressed in a cluster ( for cell type identification)?
seurat
12 days ago by
Chris
▴ 180
6
votes
6
replies
5.3k
views
How is logFC and p-value estimated (for volcano plots)?
R
edgeR
fold-Change
updated 10 days ago by
Ram
40k • written 6.5 years ago by
LRStar
▴ 200
3
votes
6
replies
436
views
Output FindMarkers()
seurat
28 days ago by
Chris
▴ 180
5
votes
6
replies
381
views
From where can I obtain vcf files of healthy exomes
exome
VCF
updated 20 days ago by
Ram
40k • written 21 days ago by
christinacanavati2014
• 0
9
votes
6
replies
1.3k
views
6 follow
Forum:
GTF files from Ensembl Releases 105 and 106 unsorted
Ensembl
bug
GTF
updated 13 days ago by
ATpoint
76k • written 10 months ago by
dlaehnemann
▴ 30
7
votes
6
replies
3.2k
views
CWL: word counting
Common-Workflow-Language
cwl
updated 14 days ago by
Ram
40k • written 6.3 years ago by
gultagr
▴ 10
8
votes
6
replies
636
views
Problems using ERCC spike-ins for normalization in DESeq2
Spike-ins
Differential-expression
DESeq2
RNA-seq
13 days ago by
manuel.fernandez
▴ 40
0
votes
6
replies
530
views
A cluster expresses two types of cells' markers in scRNA-seq
scRNA-seq
annotate
28 days ago by
feather-W
• 0
3
votes
6
replies
639
views
BWA | SAMtools | GATK debugging help
alignment
mapping
vcf
12 days ago by
TheScriptOfGilgamesh
▴ 20
1
vote
6
replies
3.2k
views
Extracting sequence, not reads, by position from bam
sequence
updated 5 days ago by
manu
• 0 • written 5.0 years ago by
geneware
▴ 10
2
votes
6
replies
497
views
Installing ensemble VEP by running INSTALL.pl takes too long.
Ensembl
VEP
updated 17 days ago by
Ben_Ensembl
★ 2.3k • written 19 days ago by
lsy9
▴ 20
3
votes
6
replies
11k
views
Retrieving data from NCBI GEO and RNA-Seq Data Analysis
RNA-Seq
R
GEO
Normalization
Count
updated 4 hours ago by
Karma
▴ 310 • written 6.1 years ago by
hkarakurt
▴ 170
0
votes
6
replies
948
views
How to run delly with multi-threading mode?
SV
calling
delly
updated 6 days ago by
bio-jr
▴ 10 • written 8 months ago by
Xi
• 0
1
vote
6
replies
590
views
Found some plasmids in my sequence. IS there any tool or process by which i can find whether there are any AMR genes within those sequence?
WGS
updated 27 days ago by
Ram
40k • written 28 days ago by
Mustafa
• 0
5
votes
6
replies
233
views
6 follow
Filter human transcription factors
transcription-factor
RNA-seq
updated 51 minutes ago by
Alex Reynolds
35k • written 17 hours ago by
Chris
▴ 180
1
vote
6
replies
567
views
How to use the Combat-seq for batch effect removal?
batch-effect
normalization
Combat-seq
updated 27 days ago by
Ram
40k • written 29 days ago by
Yoomi
• 0
8
votes
6
replies
527
views
Short Read Data Genome Assembly
spades
genome-assembly
updated 16 days ago by
ccstaats
▴ 30 • written 19 days ago by
Umer
▴ 50
6
votes
6
replies
444
views
Integration in single cell RNAseq: What does it mean?
Single
cell
updated 26 days ago by
Chris
▴ 180 • written 26 days ago by
synat.keam
▴ 80
7
votes
6
replies
10k
views
7 follow
Blastn Segmentation Fault
blast
updated 20 days ago by
Amirhossein Hajianpour
▴ 40 • written 11.8 years ago by
Srihari
▴ 30
1
vote
6
replies
574
views
Batch correction in DESeq2 - limited impact for unsupervised downstream analyses
deseq2
13 days ago by
Jane
• 0
2
votes
5
replies
262
views
How to change from gene_id to GeneID/EntrezID using R
identifiers
Deseq2
GeneID
updated 22 hours ago by
Kevin Blighe
86k • written 2 days ago by
Nicolas
• 0
0
votes
5
replies
354
views
manhattan plot with vcf information
R
manhattan
vcf
updated 4 days ago by
dthorbur
▴ 550 • written 7 days ago by
sooni
▴ 10
6
votes
5
replies
679
views
ChIP-seq visualization: Is it valid to do a coverage normalization in addition to applying a spike-in-derived scaling factor?
ChIP-seq
normalization
scaling-factor
coverage
spike-in
updated 20 days ago by
Ram
40k • written 26 days ago by
kalavattam
▴ 180
0
votes
5
replies
574
views
Bowtie2 with secondary alignment option produces multiple mapping with offset and varying alignment scores
bowtie2
score
alignment
multiple-alignment
22 days ago by
polag01
▴ 10
9
votes
5
replies
4.2k
views
CWL: how to set default values
Common-Workflow-Language
cwl
updated 14 days ago by
Ram
40k • written 6.9 years ago by
bird77
▴ 80
13
votes
5
replies
966
views
Annotating TSS: By Transcript or by Gene? Code Validation Help Needed!
genome
bed
transcript
TSS
updated 9 days ago by
i.sudbery
17k • written 4 months ago by
Rafael Soler
★ 1.2k
1
vote
5
replies
1.4k
views
--preserve_environment with docker containers?
cwltool
Common-Workflow-Language
cwl
updated 14 days ago by
Ram
40k • written 6.0 years ago by
Biowoogles
▴ 20
1
vote
5
replies
667
views
Mugsy percentage of identity
Mugsy
Genome-alignment
updated 4 days ago by
Ram
40k • written 2.5 years ago by
A_heath
▴ 140
4
votes
5
replies
588
views
Help with error scanpy
scanpy
12 days ago by
Chris
▴ 180
0
votes
5
replies
458
views
Convert gene id's to gene symbol preserving gene id's in deseq2
ensembl
r
DE
deseq2
updated 9 days ago by
Ram
40k • written 11 days ago by
dylannicoembros
• 0
775 results • Page
3 of 16
Recent Votes
How to identify 16s sequences from binning data(contigs)?
geom_signif() uses t-test to compare between more than 3 groups... Isn't this wrong?
Answer: Filter transcription factors
Comment: Calculation of TMB on gene level
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool?
Comment: ATAC-seq troubleshoot - Just Noise
t2t human reference genome for RNA-seq
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Recent Replies
Comment: how to create a loop in R
by
Nicolas Rosewick
10k
Not really a bioinformatics related question. Start by looking at R tutorial, there is plenty of them online e.g. : https://www.statmethods…
Comment: Violin plot (Monocle 3) - Troubleshooting
by
fracarb8
★ 1.2k
You did not add the screenshot.
Answer: BED files
by
Alex Reynolds
35k
Generically via `bedmap`: ``` bedmap --echo --echo-map --count exome.bed annotations.bed > answer.bed ``` The `annotations.bed` fil…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr
by
dariober
14k
It seems to me that anova followed by HSD is a more sensible approach than applying independent t-tests. Granted this is the first time I s…
Comment: BED files
by
barslmn
★ 1.8k
I am guessing you want the annotation files. https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/
Comment: Filter human transcription factors
by
Alex Reynolds
35k
Curious how redundant these TFs are. Jeff Vierstra has done some analysis on this to simplify model sets: https://www.vierstra.org/resource…
Comment: Read block operation failed with BAM file
by
Alex Reynolds
35k
https://github.com/samtools/htslib/pull/1676 patches a seek issue in `htslib` (upon which `samtools` and `pysam` depend)
Comment: Merging the filename with tsv files for master file
by
barslmn
★ 1.8k
Could you add samples from your files and your expected output.
Comment: Download an example of fully-imputed VCF files ?
by
barslmn
★ 1.8k
Check out the 1000 genomes project. https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/
Comment: obtaining circular RNAs' sequences from circBase
by
Barry Digby
★ 1.2k
Sorry my mistake! it’s been a minute since I’ve used these sites. Yes that it is common place, what is the goal of your analysis using th…
Comment: gene correlations in between two groups
by
ATpoint
76k
Use specialized software to analyse CRISPR/RNAi data, such as MAGeCK.
Comment: gene correlations in between two groups
by
edus_bioinfo
▴ 40
To be more clear, I have RNAi data from depmap with different cell lines and I separated them into two groups according to their EGFR mutat…
Comment: ATAC-seq troubleshoot - Just Noise
by
ATpoint
76k
You have reads, so sequencing is obviously fine. This is how the banding should look: https://kb.10xgenomics.com/hc/article_attachments/360…
Comment: Program for Overlapping DMRs (Differentially Methylated Regions) Between Groups
by
Basti
★ 1.7k
Do not use excel for bioinformatics purposes, using R you could use GRanges objects to find overlaps between your regions : https://www.bio…
Answer: Saving the output of LD pruning from SNPRelate package as a new GDS file
by
Patrick
• 0
Thank you James for the response; My problem is only if I want to use the output of LD pruning in a different software, like STRUCTURE (to …
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