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120,490 results • Page
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Read groups RNA-seq and hisat2
groups
read
just now by
frarodmar17
• 0
0
votes
0
replies
1
view
simulate a genome with specific event
simulation
genome
retrocopy
just now by
Matteo Ungaro
▴ 110
3
votes
4
replies
568
views
Help with R programming assignment
R
assignment
updated 2 hours ago by
Enzo
• 0 • written 7 months ago by
sidhanthbaru
• 0
0
votes
0
replies
27
views
HOMER findMotifsGenome.pl failed compilation
findMotifsGenome.pl
motifanalysis
HOMER
2 hours ago by
India
• 0
828
votes
169
replies
167k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 5 months ago by
Biostar
3.4k • written 8.2 years ago by
Istvan Albert
102k
0
votes
1
reply
43
views
Job:
SciLifeLab PULSE: Program for Future Leaders in Life Science (48 positions!)
Entrepreneur
Sweden
Mentoring
Postdoctoral
Leadership
2 hours ago by
Matthias Zepper
5.0k
4
votes
11
replies
5.8k
views
7 follow
BLAST Database error: Database memory map file error
makeblastdb
updated 4 hours ago by
Albert
• 0 • written 5 months ago by
Martina
• 0
1
vote
1
reply
100
views
MSA with extended alphabet
Multiple
sequence
MSA
alignment
updated 5 hours ago by
Mensur Dlakic
★ 29k • written 19 hours ago by
retzl.bernhard
• 0
0
votes
0
replies
34
views
Help with Finding SNPs in H. pylori Assembled Genomes
question
Technical
5 hours ago by
vrao
• 0
0
votes
0
replies
35
views
Reference Genome with decoy for RNAseq data processing
STAR
SALMON
RNAseq
5 hours ago by
cwwong13
▴ 40
1
vote
1
reply
76
views
multiple ATG SEQUENCE
MULTIPE
sequence
ATG
offtopic
updated 5 hours ago by
Carlo Yague
8.9k • written 6 hours ago by
Sijjil
• 0
0
votes
0
replies
49
views
Forum:
Keep SNP's with call rate greater than 30 in VCF
SNP
call
rate
ROH
genotyping
8 hours ago by
Smilesky
• 0
9
votes
10
replies
5.1k
views
7 follow
Buy PC for metagenomics
Assembly
alignment
genome
next-gen
updated 1 hour ago by
Joe
22k • written 6.6 years ago by
lugonauta
▴ 10
0
votes
0
replies
44
views
Dynamic tree cut results
clustering
DEG
9 hours ago by
Mai.Nabil
• 0
0
votes
0
replies
48
views
Significant variation in FastQ File Sizes - WES
LibraryPrep
WES
Human
13 hours ago by
irate.pirate
• 0
0
votes
2
replies
211
views
Repetitive sequences analysis
Repetitive
sequences
updated 14 hours ago by
rfran010
★ 1.3k • written 1 day ago by
frarodmar17
• 0
0
votes
1
reply
107
views
Protein secuence extraction from gpff file for a genes list
Protein
gpff
updated 15 hours ago by
JC
13k • written 17 hours ago by
reza
▴ 300
0
votes
0
replies
71
views
Job:
Postdoctoral Researcher in Single-Cell Sequencing Analysis
researcher
post-doctoral
18 hours ago by
ejvandenoord
• 0
0
votes
2
replies
157
views
filtering heterozygous genotypes
bcftools
heterozygous
10 hours ago by
analyst
▴ 60
2
votes
0
replies
119
views
An alternative to haplotype phasing - assembly?
samtools
assembly
BAM
spades
phasing
21 hours ago by
Jess
▴ 60
0
votes
0
replies
71
views
How to remove rows with empty gene symbols from a seurat object?
seurat
19 hours ago by
Chris
▴ 360
2
votes
3
replies
197
views
Affine versus Linear Alignment
linear-alignment
affine-score
updated 21 hours ago by
Ram
44k • written 22 hours ago by
per
• 0
0
votes
0
replies
66
views
how to make/get the SNP annotation file for running TORUS
TORUS
Annotation
SNP
GWAS
updated 21 hours ago by
GenoMax
149k • written 22 hours ago by
lee
• 0
0
votes
1
reply
105
views
Flongle 16srRNA nanopore sequencing
R.9.4.1
flow
flongle
updated 21 hours ago by
GenoMax
149k • written 22 hours ago by
Major ginger
• 0
0
votes
2
replies
150
views
Genomes with existing T2T assemblies?
T2T
genome
assembly
reference
updated 23 hours ago by
cmdcolin
★ 4.1k • written 1 day ago by
predeus
★ 2.1k
0
votes
1
reply
373
views
R CytoTRACE2 Results: Potency Score of Naive B Cells Lower Than Memory B and Plasmablasts – Contradicts Biological Knowledge
CytoTRACE2
updated 20 hours ago by
yura.grabovska
▴ 690 • written 23 hours ago by
Binghong
▴ 20
1
vote
2
replies
206
views
Installing ggpubr in Docker container rocker/r-base??
ggpubr
dockerfile
docker
r
updated 21 hours ago by
Ram
44k • written 1 day ago by
giulia.trauzzi
▴ 30
0
votes
0
replies
63
views
News:
Bayesian Data Analysis in R course - online, March 3-7
Bayesian
Statistics
R
1 day ago by
Physalia-courses
★ 2.6k
4
votes
5
replies
234
views
Should we cite sed / awk in papers?
sed
awk
updated 22 hours ago by
ATpoint
87k • written 1 day ago by
amy__
▴ 250
0
votes
0
replies
57
views
Briggs model parametes
Briggs
damage
Gargammel
1 day ago by
anna.utili
• 0
3
votes
7
replies
315
views
Nanopore sequencing - plasmid assembly length confusion
assembly
long
nanopore
reads
3 hours ago by
abedkurdi10
▴ 190
0
votes
0
replies
79
views
Post-GWAS colocalization analysis VS. variant annotation, what's the difference?
variant
colocalization
snp
annotation
GWAS
3 hours ago by
sarfdezco
• 0
0
votes
0
replies
82
views
EDTA ,Transposon detection, repeat modeler and masker
homology_based_TE_detection
fragmentedTE
1 day ago by
manaswiniparija3
▴ 50
2
votes
8
replies
512
views
Finding ORFs in a FASTA file
MatrixScore
ORFs
Motifs
MotifScoring
updated 1 day ago by
Michael
55k • written 5 days ago by
Melissa
• 0
2
votes
3
replies
208
views
Ilumina Low quality bases at first 20 cycles + PHIX problem
Sequencing
updated 1 day ago by
GenoMax
149k • written 2 days ago by
alenew.am
▴ 10
0
votes
3
replies
170
views
HMP dataset download issue (403 error)
HMP
dataset
microbiome
updated 1 day ago by
GenoMax
149k • written 1 day ago by
Emily
▴ 70
0
votes
1
reply
118
views
Enrichment Analysis for cCREs
Enrichment
statstest
bedtools
cCREs
fishers
updated 1 day ago by
ATpoint
87k • written 1 day ago by
alexanderturco1
• 0
0
votes
0
replies
103
views
Job:
Postdoctoral Research Position: Developing Novel Algorithms and Tools for Circular RNA Analysis
circRNAs
biology
bioinformatics
computational
1 day ago by
Tobias Jakobi
• 0
6
votes
10
replies
677
views
Per Sequence GC Content fail
fastqc
23 hours ago by
Eduardo
• 0
0
votes
10
replies
357
views
6 follow
Phylogenetic tree from whole genome using BUSCO
BUSCO
whole_genome
phylogenetic_tree
updated 1 day ago by
shelkmike
★ 1.5k • written 2 days ago by
manaswiniparija3
▴ 50
8
votes
7
replies
6.4k
views
has anyone use trimmomatic with NEBNext adaptors
rna-seq
updated 1 day ago by
Johan Zicola
▴ 80 • written 6.3 years ago by
eozcan
▴ 10
2
votes
1
reply
140
views
t2t RNAseq alignment with STAR
chm13
t2t
RNAseq
updated 1 day ago by
GenoMax
149k • written 1 day ago by
eva_u
▴ 30
2
votes
0
replies
152
views
Herald:
The Biostar Herald for Wednesday, February 19, 2025
herald
2 days ago by
Biostar
3.4k
1
vote
2
replies
175
views
Cell Type annotation showing Normal cells as Cancer cells in single cell analysis.
seurat
Single_cell
spatial-transcriptomics
updated 2 days ago by
GenoMax
149k • written 2 days ago by
geno89
▴ 10
0
votes
0
replies
101
views
Running NGSadmix with pre-calculated ancestral genotype freqs?
admixture
ngsadmix
lcwgs
angsd
2 days ago by
j.smout.1
• 0
5
votes
5
replies
385
views
Differential Expression and absolute expression
normal
DEG
tumour
rna
2 days ago by
jain72744
▴ 10
0
votes
3
replies
273
views
Mapping ~100-300bp Sequences to Metagenome-Assembled Genomes
assembly
Metagenomic
updated 1 day ago by
GenoMax
149k • written 2 days ago by
chemokine-1
▴ 10
0
votes
1
reply
152
views
Differetial analysis EdgeR
Differetial
EdgeR
analysis
updated 2 days ago by
ATpoint
87k • written 2 days ago by
maryak
▴ 20
0
votes
3
replies
182
views
Can I compare Gene Expression in T Cells from PBMCs vs. Tumor Tissue (for match samples)?
batch-effect-correction
integration
scRNAseq
single-cell
harmony
updated 2 days ago by
ATpoint
87k • written 2 days ago by
Saeedeh Salehi
▴ 10
1
vote
0
replies
141
views
Rules for Assigning Start and End Phase to Coding Exons
stare_phase
reading_frame
end_phase
2 days ago by
Milica
▴ 10
120,490 results • Page
1 of 2410
Recent Votes
Comment: Compare genomes of different species and published studies (different years, seq
An alternative to haplotype phasing - assembly?
Answer: Off-target % for whole-exome sequencing panel
Answer: MSA with extended alphabet
Comment: multiple ATG SEQUENCE
A: remove empty reads from fastq files
Comment: Should we cite sed / awk in papers?
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Comment: Buy PC for metagenomics
by
Joe
22k
How big are the internal drives? You have at least a terabyte of raw data by the sounds of it, and you can probably assume you'll need at …
Comment: SciLifeLab PULSE: Program for Future Leaders in Life Science (48 positions!)
by
Matthias Zepper
5.0k
PS: There's a catch: Swedish mentality is very different from the US. It is generally considered polite to be tolerant and to mind your o…
Answer: BLAST Database error: Database memory map file error
by
Albert
• 0
I had the same problem. The path to the fasta file contained a space. After moving the fasta file to a folder without spaces in the path I …
Answer: MSA with extended alphabet
by
Mensur Dlakic
★ 29k
I think it is unlikely you will find a pre-packaged solution to that problem. At the very least you will have to devise a scoring matrix (A…
Comment: multiple ATG SEQUENCE
by
Carlo Yague
8.9k
This post does not fit the theme of this forum. You should try to ask your question on a biology forum such as biology.stackexchange.com in…
Comment: Nanopore sequencing - plasmid assembly length confusion
by
abedkurdi10
▴ 190
The plasmid was extracted using maxiprep kit from Qiagen. Regarding the library preparation, rapid barcoding kit from ONT (SQK.RBK.114.24) …
Comment: Buy PC for metagenomics
by
Mensur Dlakic
★ 29k
I think you should consider at least doubling the RAM size, and 256 GB would be even better. Back in 2016 I bought almost the same computer…
Answer: Buy PC for metagenomics
by
Pratibha kadam
• 0
I am into a same situation. We are planning to do a longitudinal shotgun metagenomic study where 400 samples (3-4 GB per sample ) will b…
Comment: filtering heterozygous genotypes
by
analyst
▴ 60
No i mean heterozygosity such as 'GT="het"'
Answer: Repetitive sequences analysis
by
rfran010
★ 1.3k
I recommend the Hammell lab GTF files: https://www.dropbox.com/scl/fo/jdpgn6fl8ngd3th3zebap/ALDQ94uFrf3r1QM1zoT9jHU/TEtranscripts?dl=0&r…
Answer: Repetitive sequences analysis
by
JC
13k
You can convert the RM output (https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.out.gz) to a valid GTF with some script but …
Answer: Protein secuence extraction from gpff file for a genes list
by
JC
13k
This is the first time I've heard about this format but seems a GBK modified for proteins, you can parse with some Perl: #!/usr/bin/…
Answer: filtering heterozygous genotypes
by
Pierre Lindenbaum
165k
> How can I modify above command to retain genotypes with heterozygosity < 0.2 ? you meant Allele Frequency ? if INFO/AF is defined …
Comment: R CytoTRACE2 Results: Potency Score of Naive B Cells Lower Than Memory B and Pla
by
yura.grabovska
▴ 690
I think expression-based estimations like "potency score" and the broader concept of trajectories are prone to being affected by the rate o…
Comment: Affine versus Linear Alignment
by
Ram
44k
I was wrong - I eyeballed it and missed a few gap openings - you are correct, there are 5 openings. So the total is 5 opens (-50) + 3 ext (…
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