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Limit : this week
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231 results • Page
2 of 5
Sort: Votes
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Votes
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2
votes
5
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974
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Why multiple SYMBOLS, Consequences... for Variant Effect Predictor (VEP)
VEP
updated 1 day ago by
barslmn
★ 2.1k • written 15 months ago by
gernophil
▴ 80
2
votes
3
replies
236
views
Extracting information from my VCF file
VCF
updated 1 day ago by
bioruffo
▴ 40 • written 1 day ago by
realtreeecat
• 0
2
votes
2
replies
291
views
Seeking help with Tcga Target Gtex Expected Count Data
R
TCGA
gTEX
4 days ago by
bioinfo_enthusiast
• 0
2
votes
1
reply
1.1k
views
Using the ranking value to filter
discosnp
RNA-Seq
variant-calling
updated 1 day ago by
Ram
43k • written 6.0 years ago by
vguerracanedo
▴ 10
2
votes
2
replies
212
views
Seeking Help with Cell Ranger Multi Error in fixed-RNA-profiling
chromium
fixed-RNA-profiling
cellranger
updated 6 days ago by
naveau
• 0 • written 13 days ago by
lam
▴ 10
2
votes
5
replies
450
views
Searching for gene in multiple genomes
gene
genome
alignment
sequence
updated 5 days ago by
BioinfGuru
★ 1.6k • written 6 days ago by
Miya
• 0
2
votes
2
replies
200
views
Location of NCBI ftp site changed?
ftp
ncbi
1 day ago by
sampsa.hyvamaki
• 0
2
votes
4
replies
1.6k
views
bowtie2 maximum value of MAPQ
bowtie2
bowtie
updated 3 days ago by
axol0tl
• 0 • written 3.6 years ago by
sami
▴ 30
2
votes
5
replies
1.8k
views
alignement and Variant calling with BWA and samtools
variant-calling
samtools
BWA
updated 1 day ago by
Ram
43k • written 2.9 years ago by
simon.burgermeister
▴ 30
2
votes
2
replies
257
views
Annotating indels and SNVs
annotation
indels
SNV
6 days ago by
am29
▴ 30
2
votes
1
reply
2.5k
views
CRAM reference registry and the GRch38 reference genome
BAM
Samtools
GRCh38
CRAM
Variant-Calling
updated 1 day ago by
Ram
43k • written 5.3 years ago by
Mehulsharma.253
▴ 30
2
votes
3
replies
446
views
Should I use Dfam or a custom repetitve elements library (from PlantRep) as a repeat database; using RepeatMasker in a Linux machine?
genome
sequence
repeatmasker
blast
updated 1 day ago by
b.contreras.moreira
▴ 70 • written 2 days ago by
Vijith
▴ 30
2
votes
11
replies
802
views
RNA seq aligner?
Alignment
3 days ago by
tesfaye
• 0
2
votes
1
reply
207
views
Disease Prevalence Database/Disease Incidence Database
prevalence
updated 6 days ago by
Ram
43k • written 7 days ago by
Shicheng Guo
★ 9.4k
2
votes
3
replies
252
views
Hybrid assembly Pacbio- Nanopore
long-reads
hybric
assembly
genome
short-reads
updated 4 hours ago by
colindaven
6.3k • written 2 days ago by
Lissa Cruz Saavedra
• 0
2
votes
4
replies
349
views
Visualizing human genomic loci
Genome
visualization
2 days ago by
James
▴ 10
2
votes
3
replies
213
views
Reference mouse phased vcf
mm10
vcf
phasing
Beagle
3 days ago by
machoo
• 0
2
votes
1
reply
300
views
Tool:
TGSFilter, An ultra-fast and efficient tool for long reads filtering and trimming
genome-assembly
filtering
reads
trimming
updated 3 days ago by
Yingzi
• 0 • written 4 days ago by
Huiyang
▴ 180
2
votes
12
replies
355
views
Variant calling of GBS data
GBS
variants
BQSR
2 hours ago by
analyst
▴ 10
1
vote
2
replies
233
views
Kmers unique mapping
KMC
alignment
bowtie
kmers
5 days ago by
enee
▴ 10
1
vote
3
replies
324
views
Combining and Forward and Reverse Reads
genome
alignment
concatenation
sequencing
3 days ago by
SineWave
• 0
1
vote
5
replies
442
views
Not getting any modification calls in nanopore reads with dorado basecaller
mofications
dorado
basecalling
nanopore
methylation
updated 6 days ago by
LauferVA
4.1k • written 6 days ago by
njornet
▴ 10
1
vote
2
replies
170
views
vg call is time consuming
vg
18 hours ago by
Maxine
▴ 40
1
vote
3
replies
745
views
Can shotgun metagenome approaches effectively target both RNA and DNA viruses in low-viral-load water samples?
RNA-virus
binning
metagenome
abundance
shotgun
updated 4 days ago by
joe
▴ 470 • written 6 days ago by
mathavanbioinfo
▴ 80
1
vote
1
reply
472
views
Help with SCENIC+
scenic-plus
updated 4 days ago by
corbettberry
▴ 10 • written 5 months ago by
Chris
▴ 260
1
vote
2
replies
343
views
What is meant by 'genomic order' in gatk's GatherVcfs, and how do I check for it?
gatk
vcf
merge
updated 4 days ago by
Pierre Lindenbaum
160k • written 4 days ago by
8armed
• 0
1
vote
2
replies
347
views
How to extract unmapped reads to assemble a plasmid
plasmid
transconjugant
reference-genome
4 days ago by
Barbara
• 0
1
vote
3
replies
1.2k
views
esearch get taxonomy ID from a large list of accession IDs
esearch
ubuntu
updated 1 day ago by
Bertalan_Takacs
▴ 90 • written 20 months ago by
garfield320
▴ 20
1
vote
2
replies
913
views
Jupyter notebook installation
Jupyter
updated 1 day ago by
chictu
▴ 10 • written 7 months ago by
sarahmanderni
▴ 100
1
vote
2
replies
217
views
Is it possible to see so little adipocyte in white adipose tissue?
scRNA-seq
1 day ago by
kayah
• 0
1
vote
1
reply
199
views
DESeq2 and normalization
RNA-seq
normalization
DESeq2
updated 1 day ago by
GenoMax
140k • written 1 day ago by
JH
• 0
1
vote
10
replies
689
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 9 hours ago by
GenoMax
140k • written 5 weeks ago by
Sky
▴ 10
1
vote
2
replies
222
views
Deseq generating warning "the model matrix is not full rank"
deseq
updated 1 day ago by
bioruffo
▴ 40 • written 2 days ago by
MAPK2
▴ 40
1
vote
2
replies
227
views
BWA MEM Alignment mapped small part of the reads!!
bwa
mem
updated 1 day ago by
bioruffo
▴ 40 • written 2 days ago by
Bunit
• 0
1
vote
0
replies
95
views
Job:
Job Opening - Fred Hutch - Director of Training & Community
fred-hutchinson
updated 1 day ago by
Ram
43k • written 2 days ago by
Fred Hutch (Recruiting)
▴ 20
1
vote
6
replies
461
views
Quest about the input data for PCA analysis
PCA
5 days ago by
tujuchuanli
▴ 100
1
vote
6
replies
2.4k
views
Variant calling from multiple sequencing runs for a single samples
variant-calling
updated 1 day ago by
Ram
43k • written 6.9 years ago by
harish.nucl
• 0
1
vote
1
reply
169
views
Forum:
Can I use this community for software development?
software-development
updated 2 days ago by
Ram
43k • written 3 days ago by
avpuzanov
• 0
1
vote
2
replies
1.2k
views
Multi-fasta file for gffread
gffread
gtf
fasta
updated 6 days ago by
alnam
▴ 10 • written 2.4 years ago by
Vitor1
▴ 120
1
vote
1
reply
1.4k
views
Lowercase variants reported by SomaticSniper
variant-calling
SomaticSniper
updated 1 day ago by
Ram
43k • written 6.7 years ago by
Inés Sentís
▴ 10
1
vote
2
replies
923
views
How to display gene expression after Harmony correction in scRNA-seq analysis
scRNA-seq
correction
Harmony
5 days ago by
tujuchuanli
▴ 100
1
vote
13
replies
963
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
updated 2 days ago by
lcj34
▴ 410 • written 8 days ago by
b.contreras.moreira
▴ 70
1
vote
3
replies
2.0k
views
psmc bootstrapping help
bootstrap
psmc
updated 2 days ago by
xuby963
• 0 • written 3.1 years ago by
truebeliever24
▴ 50
1
vote
1
reply
1.8k
views
Intronic Variant Filtering
variant-calling
snp
updated 1 day ago by
Ram
43k • written 6.7 years ago by
cvu
▴ 180
1
vote
1
reply
152
views
Pool-Seq same as normal variant calling?
Pool-Seq
Variant-Calling
updated 1 day ago by
dthorbur
★ 1.7k • written 2 days ago by
andrebolerbarros
• 0
1
vote
0
replies
96
views
Downloading immne signature and pathway signature genes form publication and KEGG
genes
TRANSCRIPTOME_signature
2 days ago by
mrazib0210
▴ 10
1
vote
3
replies
2.4k
views
How to remove variants with 3+ alleles present Plink1.9
HaplotypeCaller
GATK
Plink1.9
vcftools
updated 6 days ago by
Jingjingzhang
• 0 • written 2.1 years ago by
ramshahaya
▴ 10
1
vote
8
replies
335
views
0-based coordinates from samtools depth
samtools
coverage
depth
updated 2 days ago by
Pierre Lindenbaum
160k • written 3 days ago by
marco.barr
▴ 30
1
vote
0
replies
108
views
checkm lineage.ms output file
checkm
lineage
3 days ago by
A_heath
▴ 160
1
vote
1
reply
195
views
genome.fa to indix files to use it in rna-seq analysis
RNA-seq
hisat2
index
updated 5 days ago by
GenoMax
140k • written 5 days ago by
Hasan_Daaboul
• 0
231 results • Page
2 of 5
Recent Votes
Comment: struggle to get fasta files from ucsc goldenPath
Answer: diffbind : killed dba.count(DBsample, bParallel=FALSE)
Quantile normalizing prior to or after TPM scaling?
Structural variant filtering
Trouble with bedtools getfasta
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Answer: Hybrid assembly Pacbio- Nanopore
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Recent Replies
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
Can you select the output format as sequence instead of BED?
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
Could you please elaborate how to retrieve the sequences directly from the table browser? Thanks!
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
If coordinates in your BED file refer to chromosomal locations then you need to use the whole genome file and get those sections by the met…
Comment: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
by
Istvan Albert
100k
maybe it would work better to ask the OP to post their question as a new one and delete this answer after, if you delete the post they ca…
Comment: Issue with making local BLAST database
by
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140k
By default only 20 entries are returned if you don't set the `retmax` parameter. You will not want to do this via R since you will be limit…
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
So this is my approach: I want to interrogate gene PVT1, I know the coordinates for it is chr8:127794532-128101252 In UCSC table I selected…
Comment: Flow Cytometry Data Analysis by Seurat
by
ATpoint
81k
> I think Seurat is suitable for our purpose (e.g. conducting dimensional reduction of the data such as tSNE), but does it make sense? No…
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
mRNA file is not going to have the same co-ordinates as the main chromosomes. Can you clarify what coordinates are in your BED file?
Comment: Downloading a list of all refseq assembly ids, including supressed assembliey
by
GenoMax
140k
Can you provide examples of suppressed ID's?
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
It is because I want to pull the mRNA fasta files and not DNA (which I guess is the case if I pull it from the entire genome)
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
If your intervals are for main chromosomes why are you using the mRNA file instead of the entire genome? If you have the gene ID's you coul…
Answer: diffbind : killed dba.count(DBsample, bParallel=FALSE)
by
Pierre Lindenbaum
160k
I downsampled the bams and it works now...
Answer: ONT direct RNA sequencing
by
dthorbur
★ 1.7k
You can check the validity of gzipped files using `gzip -v -t file.gz`. Should look something like this: ``` $ gzip -v -t test_file.…
Comment: Nanopore data filtering using fastp
by
emilydolivo97
• 0
I tested seqtk sample but I generate a wird result. Can I share my code and results with you please ?
Comment: Nextflow ERROR : Timeout waiting for connection from pool
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140k
As best as I can tell it is a combination of things. Did you try setting `export NXF_ENABLE_VIRTUAL_THREADS="true"` in your shell? You also…
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