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178 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 22 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 6 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 4 days ago by
Ruqaiya
• 0 • written 11.9 years ago by
lh3
33k
22
votes
15
replies
10k
views
12 follow
Alternatives To Liftover
liftover
genome
mapping
updated 5 days ago by
Thanujay S
• 0 • written 12.6 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
849
views
7 follow
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 5 days ago by
i.sudbery
19k • written 4 weeks ago by
Estevão
▴ 10
3
votes
11
replies
5.3k
views
6 follow
txt file to bigwig
MEME
bigwig
updated 8 minutes ago by
sogand
• 0 • written 8.6 years ago by
tanni93
▴ 50
2
votes
11
replies
790
views
ComplexHeatmap - How to change fontsize of rowAnnotation
r
ComplexHeatmap
updated 1 day ago by
Ram
44k • written 11 days ago by
hannes.bongartz
• 0
4
votes
11
replies
968
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
6 days ago by
J
▴ 10
1
vote
10
replies
647
views
Add stats to the plot
R
6 days ago by
Ghada
• 0
8
votes
10
replies
3.2k
views
8 follow
Venter Genome Vcf
vcf
updated 18 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
2
votes
10
replies
489
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
just now by
Assa Yeroslaviz
★ 1.9k
5
votes
9
replies
3.2k
views
Delete some INFO header lines and columns data
vcf
bash
vcftools
updated 13 hours ago by
tomas4482
▴ 400 • written 2.3 years ago by
pablo.goiko
• 0
1
vote
9
replies
245
views
Error with pheatmap - 'from' must be a finite number
pheatmap
r
deseq2
updated 8 minutes ago by
Ram
44k • written 16 hours ago by
vmpsb
• 0
3
votes
8
replies
885
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
3
votes
7
replies
411
views
Z score
Z-score
updated 5 hours ago by
ATpoint
82k • written 5 days ago by
Akash D
▴ 60
2
votes
7
replies
611
views
KEGG analysis in R
KEGG
clusterProfiler
Zea-mays
updated 6 days ago by
letizia.ottaviani
• 0 • written 6 weeks ago by
sansan_96
▴ 90
2
votes
7
replies
1.6k
views
Problems when trying to use ensembl-vep
ensembl
ensembl-vep
docker
updated 7 hours ago by
tomas4482
▴ 400 • written 10 months ago by
langziv
▴ 50
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
1
vote
7
replies
403
views
samtools write-index
samtools
1 day 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
0
votes
6
replies
525
views
How to build ribosomal interval files to use in CollectRnaSeqMetrics for hg38.p14
hg38.p14
ribosomal-intervals
3 hours ago by
naaj
• 0
0
votes
6
replies
295
views
from CRAM to fastq
FASTQ
WGS
CRAM
updated 5 days ago by
ATpoint
82k • written 6 days ago by
machaalani29
• 0
2
votes
6
replies
432
views
Harmony integration group.by.var parameter
single-cell
harmony
updated 1 day ago by
jared.andrews07
★ 17k • written 4 days ago by
Picasa
▴ 640
3
votes
6
replies
356
views
Problem in getting geo file through GEOQUERY
geoquery
Geo
updated 5 days ago by
Ram
44k • written 6 days ago by
anasjamshed
▴ 120
4
votes
6
replies
437
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
2.3k
views
Tool:
Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
biomart
annotation
Ensembl
updated 23 hours ago by
Mike Smith
★ 2.0k • written 2.8 years ago by
Shred
★ 1.4k
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
2
votes
6
replies
332
views
How to get the ratio of allele counts from GATK derived VCF file?
Freebayes
GATK
SNP
VCF
5 days ago by
anikcropscience
▴ 230
4
votes
6
replies
340
views
Error with BiocParallel. No barcodes files found
Barcodes
scRNA-seq
SingleCellExperiment
4 days ago by
bio_info
▴ 20
3
votes
5
replies
453
views
Super ehancers
enhancers
updated 6 days ago by
jared.andrews07
★ 17k • written 26 days ago by
Oburah
• 0
3
votes
5
replies
393
views
How to scrape BioMart data from https://sorfs.ugent.be/ website
BioMart
updated 2 days ago by
Pierre Lindenbaum
162k • written 4 days ago by
QX
• 0
0
votes
5
replies
268
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
329
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
1
vote
4
replies
292
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
6 days ago by
shpak.max
▴ 50
2
votes
4
replies
362
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
20 hours ago by
Pegasus
▴ 100
3
votes
4
replies
6.3k
views
MAUVE: No gene annotations in Genbank file alignments
software-error
MAUVE
RAST
genbank
alignment
updated 5 days ago by
pramach1
▴ 40 • written 9.8 years ago by
tptacek3050
▴ 70
1
vote
4
replies
412
views
some error in building kraken2 database
metagenome
kraken2
updated 5 days ago by
GenoMax
142k • written 5 weeks ago by
Art1ess
• 0
2
votes
4
replies
1.1k
views
samtools mpileup error - 1 samples in 1 input files
samtools
BAM
mpileup
SAM
updated 20 hours ago by
Damla
• 0 • written 2.4 years ago by
joseph.kelly.94
▴ 10
0
votes
4
replies
631
views
Illumina EPIC v2 IlmnIDs and probe names
Illumina
EPIC
EPICv2
updated 50 minutes ago by
Papyrus
★ 2.9k • written 6 months ago by
christine.a.pedersen
▴ 10
0
votes
4
replies
230
views
merge overlaps and remove non overlap genomic windows
BED
intersection
overlap
5 days ago by
reza
▴ 300
2
votes
4
replies
283
views
Allele count of 2 for homoplasmic MT variants in VCF
Variant-Calling
GATK
VCF
5 days ago by
Arton
▴ 10
3
votes
4
replies
221
views
Invalid CIGAR after using bam clipOverlap
validatesamfile
cigar
bam
clipoverlap
1 day ago by
MboiTui
▴ 20
0
votes
4
replies
344
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
6 days ago by
Luqman
• 0
2
votes
4
replies
1.2k
views
Is it possible to run CibersortX with a very small number of samples?
cibersortx
5 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 5 days ago by
May Ling
• 0 • written 3.9 years ago by
Mozart
▴ 330
3
votes
4
replies
500
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 4 days ago by
fracarb8
★ 1.7k • written 11 days ago by
txema.heredia
▴ 130
3
votes
4
replies
356
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
2 days ago by
Alexandra
• 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
178 results • Page
1 of 4
Recent Votes
Comment: UMI-Tools knee-method has great influence on the results of white list
A: Fix SAM flags on quality filtered paired-end BAM file
C: Fix SAM flags on quality filtered paired-end BAM file
C: Genes inhibiting each other's expression
C: Genes inhibiting each other's expression
A: Genes inhibiting each other's expression
Answer: PacBio Raw Data File Formats
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Recent Replies
Comment: Best practices in Fungal Genome Assembly
by
samuel.a.odonnell
▴ 520
I think tools like quickmerge (or Ragtag's patch command) can help for long-read assemblies, but I would definitely avoid using them with s…
Comment: txt file to bigwig
by
sogand
• 0
Hi, I tried to delete my comment but can't see any delete/remove option here! Thanks
Comment: Error with pheatmap - 'from' must be a finite number
by
Ram
44k
You'd see a different issue if the vector being analyzed contained character entries. This is clearly a problem with NA/NaN/Inf values in t…
Comment: Error with pheatmap - 'from' must be a finite number
by
SamGG
▴ 20
Not exactly, if the matrix has been transformed into characters. Maybe I should have asked for `is.numeric()`.
Comment: How do I check if a DNA sequence of a gene is supported by RNAseq data?
by
GenoMax
142k
> bacterial genes containing phase variable short sequence repeats in their coding regions Can you describe this in a bit more detail? Are…
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2
by
jared.andrews07
★ 17k
This is exactly my point. You should not have gotten data to this state unintentionally, so you need to double-check what was done upstream…
Comment: Search within posts based on tags using the Biostars API
by
Ram
44k
Right, that's true. One way to do that would be to get the HTML output of https://www.biostars.org/tag/crispr/ and search it for the first …
Answer: Illumina EPIC v2 IlmnIDs and probe names
by
Papyrus
★ 2.9k
The ID code and the new features for the EPICv2 are explained in the Illumina documentation which you can access [here][1], in the `Infiniu…
Comment: Error with pheatmap - 'from' must be a finite number
by
Ram
44k
That answers half of what I asked you. Where's the output to the first command?
Comment: Error with pheatmap - 'from' must be a finite number
by
Ram
44k
You already have the response to the first one, so there was no need to include that.
Answer: Illumina EPIC v2 IlmnIDs and probe names
by
GenoMax
142k
The answer is provided in this Bioconductor thread: https://support.bioconductor.org/p/9156675/
Comment: Illumina EPIC v2 IlmnIDs and probe names
by
rna-seq_researcher
▴ 60
Hi, by any chance did you manage to solve this problem?
Comment: Confirmation required on how DiffBind generates union of regions (min. 1bp overl
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142k
Tagging: https://www.biostars.org/u/10855/ <!-- this is -->
Answer: Best practices in Fungal Genome Assembly
by
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★ 2.0k
The authors of the Vertebrate Genome Project published a very useful [guide](https://www.nature.com/articles/s41586-021-03451-0) for assemb…
Comment: Polygenic Risk Score calculation
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▴ 20
Then how it will be supporting risk snps in individual patient sample? and so it is like a population based study. could you please make a…
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