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174 results • Page
1 of 4
Sort: replies
Rank
Views
Votes
Replies
64
votes
25
replies
57k
views
22 follow
Download All The Bacterial Genomes From Ncbi
ncbi
updated 6 hours ago by
GenoMax
142k • written 11.4 years ago by
rehma.ar
▴ 290
13
votes
18
replies
6.3k
views
9 follow
Blastn, need help to increase speed
RNA-Seq
blastn
blast+
updated 5 days ago by
Dunois
★ 2.5k • written 3.3 years ago by
chiachoong_leong93
▴ 20
20
votes
17
replies
13k
views
17 follow
Best Practice On Variant Discovery For Bacteria?
updated 3 days ago by
Ruqaiya
• 0 • written 11.9 years ago by
lh3
33k
19
votes
15
replies
2.3k
views
Forum:
What is the amount of sequencing data produced annually?
data
research
sequencing
updated 6 days ago by
Mohamed
• 0 • written 8 months ago by
vincenthus
▴ 70
22
votes
15
replies
10k
views
12 follow
Alternatives To Liftover
liftover
genome
mapping
updated 4 days ago by
Thanujay S
• 0 • written 12.5 years ago by
woemler
▴ 170
11
votes
13
replies
6.7k
views
7 follow
log2 fold change in RNA-seq analysis
fold
log2
change
updated 4 days ago by
May Ling
• 0 • written 2.4 years ago by
wmsalsah
▴ 10
7
votes
13
replies
847
views
7 follow
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 4 days ago by
i.sudbery
19k • written 4 weeks ago by
Estevão
▴ 10
2
votes
11
replies
763
views
ComplexHeatmap - How to change fontsize of rowAnnotation
r
ComplexHeatmap
updated 1 day ago by
Ram
44k • written 10 days ago by
hannes.bongartz
• 0
4
votes
11
replies
967
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
5 days ago by
J
▴ 10
1
vote
10
replies
644
views
Add stats to the plot
R
5 days ago by
Ghada
• 0
8
votes
10
replies
3.2k
views
8 follow
Venter Genome Vcf
vcf
updated 3 hours ago by
Jeremy Leipzig
22k • written 10.1 years ago by
win
▴ 980
1
vote
10
replies
3.6k
views
Merging multiple samples in Seurat
scRNA-seq
snRNA-seq
RNA-seq
Seurat
updated 2 days ago by
Picasa
▴ 640 • written 7 months ago by
AFP3
• 0
19
votes
10
replies
7.4k
views
7 follow
T2T-CHM13 "complete" human genome gff/gtf annotation file
genomics
written 3.0 years ago by
noodle
▴ 590
3
votes
10
replies
5.2k
views
6 follow
txt file to bigwig
MEME
bigwig
updated 2 hours ago by
ATpoint
82k • written 8.6 years ago by
tanni93
▴ 50
4
votes
9
replies
674
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 6 days ago by
marco.barr
▴ 130 • written 12 days ago by
diqixiaoyaoer
▴ 20
3
votes
8
replies
882
views
Random Access remote BAM files
htslib
BAM
updated 5 days ago by
a.penatauber
• 0 • written 3 months ago by
Lucas R.F.
▴ 20
1
vote
7
replies
397
views
samtools write-index
samtools
20 hours ago by
R.L.
• 0
8
votes
7
replies
3.9k
views
6 follow
What is the best practice of scRNA workflow for multiple patients and samples using Seurat
scRNA
sing-cell RNA
seurat
integrate
updated 1 day ago by
Picasa
▴ 640 • written 3.5 years ago by
SupBioInformatics
▴ 70
2
votes
7
replies
609
views
KEGG analysis in R
KEGG
clusterProfiler
Zea-mays
updated 5 days ago by
letizia.ottaviani
• 0 • written 6 weeks ago by
sansan_96
▴ 90
3
votes
7
replies
4.0k
views
Difference in Bismark output methylation call files and coverage files
RRBS
Bismark
DNA-methylation
updated 4 days ago by
Papyrus
★ 2.9k • written 3.9 years ago by
linelr
▴ 40
2
votes
6
replies
2.2k
views
Tool:
Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
biomart
annotation
Ensembl
updated 8 hours ago by
Mike Smith
★ 2.0k • written 2.8 years ago by
Shred
★ 1.4k
4
votes
6
replies
337
views
Error with BiocParallel. No barcodes files found
Barcodes
scRNA-seq
SingleCellExperiment
3 days ago by
bio_info
▴ 20
0
votes
6
replies
290
views
from CRAM to fastq
FASTQ
WGS
CRAM
updated 5 days ago by
ATpoint
82k • written 5 days ago by
machaalani29
• 0
4
votes
6
replies
12k
views
Looking for differential gene expression between treatment, within a specific cluster (seurat)
seurat
updated 1 day ago by
jared.andrews07
★ 17k • written 4.7 years ago by
cook.675
▴ 230
1
vote
6
replies
377
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
6 days ago by
Umer
▴ 50
4
votes
6
replies
433
views
Mouse or Rat Gene Expression Data Similar to GTEx
whole-body
expression
atlas
4 days ago by
Shicheng Guo
★ 9.4k
2
votes
6
replies
417
views
Harmony integration group.by.var parameter
single-cell
harmony
updated 1 day ago by
jared.andrews07
★ 17k • written 3 days ago by
Picasa
▴ 640
3
votes
6
replies
355
views
Problem in getting geo file through GEOQUERY
geoquery
Geo
updated 5 days ago by
Ram
44k • written 6 days ago by
anasjamshed
▴ 120
2
votes
6
replies
326
views
How to get the ratio of allele counts from GATK derived VCF file?
Freebayes
GATK
SNP
VCF
4 days ago by
anikcropscience
▴ 230
3
votes
5
replies
486
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
6 days ago by
beantkapoor16
▴ 10
2
votes
5
replies
306
views
Z score
Z-score
updated 4 days ago by
Ram
44k • written 4 days ago by
Akash D
▴ 60
3
votes
5
replies
372
views
How to scrape BioMart data from https://sorfs.ugent.be/ website
BioMart
updated 1 day ago by
Pierre Lindenbaum
162k • written 3 days ago by
QX
• 0
3
votes
5
replies
453
views
Super ehancers
enhancers
updated 6 days ago by
jared.andrews07
★ 17k • written 25 days ago by
Oburah
• 0
0
votes
5
replies
260
views
Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
Bowtie
3 days ago by
Deepthi
• 0
1
vote
4
replies
410
views
some error in building kraken2 database
metagenome
kraken2
updated 4 days ago by
GenoMax
142k • written 4 weeks ago by
Art1ess
• 0
0
votes
4
replies
251
views
Where to find old version of GATK best practice
gatk
6 days ago by
Zhenyu Zhang
★ 1.2k
0
votes
4
replies
246
views
Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
GATK
UnifiedGenotyper
6 days ago by
shpak.max
▴ 50
1
vote
4
replies
288
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
6 days ago by
shpak.max
▴ 50
2
votes
4
replies
1.0k
views
samtools mpileup error - 1 samples in 1 input files
samtools
BAM
mpileup
SAM
updated 4 hours ago by
Damla
• 0 • written 2.4 years ago by
joseph.kelly.94
▴ 10
3
votes
4
replies
199
views
Invalid CIGAR after using bam clipOverlap
validatesamfile
cigar
bam
clipoverlap
15 hours ago by
MboiTui
▴ 20
3
votes
4
replies
6.3k
views
MAUVE: No gene annotations in Genbank file alignments
software-error
MAUVE
RAST
genbank
alignment
updated 4 days ago by
pramach1
▴ 40 • written 9.8 years ago by
tptacek3050
▴ 70
2
votes
4
replies
343
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
4 hours ago by
Pegasus
▴ 100
3
votes
4
replies
350
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
1 day ago by
Alexandra
• 0
0
votes
4
replies
226
views
merge overlaps and remove non overlap genomic windows
BED
intersection
overlap
5 days ago by
reza
▴ 300
2
votes
4
replies
1.2k
views
Is it possible to run CibersortX with a very small number of samples?
cibersortx
4 days ago by
Aspire
▴ 330
5
votes
4
replies
5.2k
views
6 follow
Classic threshold for log2 fold change in RNA-seq experiment
RNA-Seq
updated 4 days ago by
May Ling
• 0 • written 3.9 years ago by
Mozart
▴ 330
2
votes
4
replies
280
views
Allele count of 2 for homoplasmic MT variants in VCF
Variant-Calling
GATK
VCF
5 days ago by
Arton
▴ 10
1
vote
4
replies
324
views
Single cell analysis: Unable to subset cells in seurat object using desired nFeature_RNA cut off
single-cell
3 days ago by
sc_analysis
• 0
3
votes
4
replies
496
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 3 days ago by
fracarb8
★ 1.7k • written 11 days ago by
txema.heredia
▴ 130
0
votes
4
replies
343
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
5 days ago by
Luqman
• 0
174 results • Page
1 of 4
Recent Votes
A: Most Popular and fancy SNP analysis tools Comparison: Plink, SNPassoc, SNPRelate
Most Popular and fancy SNP analysis tools Comparison: Plink, SNPassoc, SNPRelate
GWAS analysis tool
Answer: Cut&Run and heatmap
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?
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Recent Replies
Comment: txt file to bigwig
by
ATpoint
82k
Please stop asking questions in existing threads. Delete these two comments and open a new question with all the necessary details to under…
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…
Comment: 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…
Answer: Help me with Heatmap
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…
Answer: Help me with simple data for RNA seq
by
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.
by
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…
Answer: Salmon vs Kallisto vs RSEM
by
Rob
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
• 0
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…
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