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121,957 results • Page
165 of 2440
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Votes
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0
votes
5
replies
1.4k
views
how to start DEG analysis after featurecounts
RNAseq
DEG
21 months ago by
kayah
▴ 20
0
votes
1
reply
1.0k
views
confusing results of enrichKEGG (clusterProfiler)
clusterProfiler
BgRatio
GeneRatio
enrichKEGG
updated 21 months ago by
ATpoint
89k • written 21 months ago by
Ann
▴ 40
0
votes
0
replies
546
views
How to make block alignment graph with PROGRESSIVE-MAUVE?
mauve
ubuntu
aligner
21 months ago by
marongiu.luigi
▴ 760
3
votes
12
replies
2.3k
views
why 99% reads failed to align in mir-seq analysis?
Fastqc
bowtie1
miRNA-seq
alignment
differential-expression-analysis
21 months ago by
mohammadhassanj
▴ 260
0
votes
3
replies
946
views
Hisat2 error not recognising files Trimmed files
Hisat2
updated 21 months ago by
ATpoint
89k • written 21 months ago by
Mickey
• 0
0
votes
0
replies
565
views
News:
3rd edition of the Winter School in Bioinformatics - Online February 26 - March 1
genomics
reproducibility
phylogenomics
transcriptomics
21 months ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
441
views
nanopore data analysis methylation modification
6mA
mCaller
ONT
methylation
21 months ago by
Domi
• 0
50
votes
20
replies
4.0k
views
10 follow
Forum:
First experiences matter
first-time
tolerance
updated 21 months ago by
Michael Love
★ 2.6k • written 21 months ago by
Mensur Dlakic
★ 30k
0
votes
2
replies
1.0k
views
Tool to Create Sequence Logo Plot with Indels or Alignment-Aware Position Frequency Matrix
sequence-logo
updated 21 months ago by
Ram
45k • written 21 months ago by
Charles-Alexandre Roy
▴ 70
2
votes
1
reply
766
views
need some recommendation for missense mutation insilico analysis
mutation
updated 21 months ago by
Ram
45k • written 21 months ago by
sindy_roby
• 0
4
votes
8
replies
4.7k
views
Install STAR on MacBook Pro M1
STAR
Genomics
MacBookProM1
updated 21 months ago by
Ram
45k • written 21 months ago by
yklee2083
• 0
0
votes
0
replies
494
views
Kraken2 with Humann3
humann3
kraken2
21 months ago by
manekineko
▴ 10
3
votes
12
replies
12k
views
7 follow
Remove ensembl identifiers from Seurat
seurat
rstudio
RNA-Seq
updated 21 months ago by
TigerSheng
• 0 • written 5.3 years ago by
V
▴ 420
0
votes
0
replies
542
views
Single cell analysis of pre- and post treatment
scRNA-seq
NGS
RNA-Seq
updated 21 months ago by
Ram
45k • written 21 months ago by
Researcher
▴ 30
0
votes
1
reply
616
views
gene family analysis
gene-family
updated 20 months ago by
Ram
45k • written 21 months ago by
3518835972
• 0
0
votes
3
replies
1.2k
views
Calculating number of SNPs in linkage disequilibrium at different thresholds from 1000 genomes project using PLINK
PLINK
linkage
SNP
LD
disequilibrium
updated 21 months ago by
Ram
45k • written 21 months ago by
octopuslegs11
▴ 10
0
votes
3
replies
938
views
substring BAM alignments from read direction
CIGAR
BAM
21 months ago by
June
▴ 20
1
vote
1
reply
747
views
stacks . vcf . admixture , structure extract data from vcf ?
radseq
stacks
structure
updated 21 months ago by
Pierre Lindenbaum
166k • written 21 months ago by
csag6433
• 0
0
votes
0
replies
425
views
identify SNPs locations
Chip-seq
histonemarks
Enhancers
21 months ago by
Faiza
▴ 10
3
votes
2
replies
1.4k
views
question about illumina adapter sequences
Illumina
adapter
sequencing
21 months ago by
Meghan.T
▴ 10
0
votes
0
replies
854
views
News:
course - Reproducibility in Bioinformatics
Docker
Reproducibility
written 2.5 years ago by
Physalia-courses
★ 2.6k
1
vote
3
replies
1.3k
views
Difference between clipping and without clipping in Fastq-dump
SRAtoolkit
updated 21 months ago by
ATpoint
89k • written 21 months ago by
CTLong
▴ 140
0
votes
1
reply
5.1k
views
Seurat v5 subsetting object based on gene counts
seuratv5
Seurat
single-cell
21 months ago by
f-bee
• 0
0
votes
3
replies
1.0k
views
Why does GATK thinks directory is BAM index file?
GATK
Galaxy
21 months ago by
ben
• 0
0
votes
0
replies
636
views
maftools do not find differentially mutated genes while bcftools isec have a lot of locus for each compared sample
bcftools
maftools
compare
vcf
21 months ago by
omicsresearch
• 0
2
votes
4
replies
1.3k
views
Help with vcf annotation
Vcf
dbsnp
annotation
21 months ago by
HoWI
• 0
0
votes
0
replies
660
views
BigWig file Normalization
Bigwig
file
21 months ago by
daffodil
▴ 10
0
votes
1
reply
556
views
Efficiently Adding Missing 0/0 Sites to VCF from Whole-Genome Sequencing
vcf
updated 21 months ago by
Pierre Lindenbaum
166k • written 21 months ago by
Tobias
• 0
0
votes
2
replies
822
views
From nucleotide or proteine sequences to EC number using biopython
ECnumber
21 months ago by
friguiahlem8
▴ 30
1
vote
1
reply
981
views
Bamutils/ClipOverlap
Bamutils
ClipOverlap
updated 21 months ago by
GenoMax
154k • written 21 months ago by
chrisk
• 0
0
votes
0
replies
442
views
Nuclesome visualization
Nucleosome
MNase
DANPOS
21 months ago by
jetson
• 0
0
votes
1
reply
1.1k
views
Variant calling from Mitochondrial Genome
Variant-Calling
NGS
Mitochondria
updated 18 months ago by
Ram
45k • written 21 months ago by
adarsh
▴ 60
0
votes
0
replies
413
views
ONT cDNA data processing with Pinfish
pinfish
updated 20 months ago by
Ram
45k • written 21 months ago by
wqqgenetics
• 0
12
votes
22
replies
6.9k
views
Can anyone simplify GATK installation
GATK
21 months ago by
Tundup
▴ 10
3
votes
2
replies
1.5k
views
Method of combining replicate data for signal track visualization
ATAC-seq
UCSC
IGV
updated 21 months ago by
Maximilian Haeussler
★ 1.8k • written 21 months ago by
Orange
▴ 30
2
votes
6
replies
1.9k
views
Error with fastq file corruption when downloading from SRA explorer using SLURM job
SRAExplorer
corruption
rna-seq
SLURM
21 months ago by
biotrekker
▴ 110
2
votes
2
replies
917
views
masurca invalid forward file for PE library
masurca
assembly
illumina
21 months ago by
m.t.lorenc
• 0
0
votes
0
replies
406
views
recessive model in saige
GWAS
21 months ago by
ccagg
▴ 60
0
votes
2
replies
851
views
Proteomic data search and analysis
Proteomics
updated 4 months ago by
ehaag
▴ 100 • written 21 months ago by
abba647
▴ 10
0
votes
1
reply
974
views
readNanoStringRccSet does not accept non-unique values phenoDataRccColName
NanoStringNCTools
NanoString
nanostringr
updated 21 months ago by
Kevin Blighe
89k • written 3.3 years ago by
sangeetashukla
• 0
1
vote
5
replies
1.5k
views
RNA-seq pipeline
snakemake
Ubuntu
21 months ago by
Javier
• 0
0
votes
1
reply
727
views
Sheep-Human ortholog mapping with BioMart and Orthogene/Gprofiler
ortholog
sheep
updated 18 months ago by
Shuang He
• 0 • written 21 months ago by
Michael
• 0
3
votes
5
replies
1.7k
views
ATAC-Seq and featureCounts
ATAC-Seq
featureCounts
updated 21 months ago by
ATpoint
89k • written 21 months ago by
qudrat.nii
▴ 40
4
votes
1
reply
2.7k
views
Salmon quant with netflow nf-core/rnaseq -r 3.13.2
Salmon
nextflow
updated 21 months ago by
Barry Digby
★ 1.3k • written 21 months ago by
Hojn
▴ 30
2
votes
4
replies
1.6k
views
VEP filtering query
ensembl-vep
21 months ago by
prasundutta87
▴ 720
2
votes
2
replies
1.4k
views
DiffBind dba.contrast with design and/or categories parameters
ATAC
DiffBind
updated 21 months ago by
GenoMax
154k • written 21 months ago by
Orange
▴ 30
2
votes
3
replies
1.5k
views
Filtering long read data
dorado
alignment
filtering
QC
nanopore
21 months ago by
eebloom
▴ 110
4
votes
2
replies
1.4k
views
BigWig file in IGV
IGV
updated 21 months ago by
Ram
45k • written 21 months ago by
daffodil
▴ 10
0
votes
3
replies
1.4k
views
Problems running Roary
pangenome
Roary
updated 21 months ago by
Ram
45k • written 21 months ago by
SushiRoll
▴ 140
3
votes
4
replies
1.3k
views
Is mir-seq reads quality good (Fastqc report) for DE analysis?
transcriptome
Fastqc
miRNA-seq
differential-expression-analysis
RNA-seq
updated 21 months ago by
GenoMax
154k • written 21 months ago by
mohammadhassanj
▴ 260
121,957 results • Page
165 of 2440
Recent Votes
FastTrack Bioinformatics - Online Course in Bioinformatics
Comment: limmaFit error when comparing TCGA RNA-Seq data
A: The Biostar Handbook. A bioinformatics e-book for beginners.
Modernized RNA-MuTect pipeline for tumor-only RNA-seq somatic variant calling
Dictys refuses to use CUDA supported pytorch during installation
Answer: Dictys refuses to use CUDA supported pytorch during installation
Comment: Looking to learn practical bioinformatics
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Recent Awards •
All
Popular Question
to
sacha
★ 2.5k
Popular Question
to
Guilherme
• 0
Commentator
to
GenoMax
154k
Popular Question
to
Ibrahim Tanyalcin
★ 1.2k
Teacher
to
colindaven
8.0k
Popular Question
to
m90
▴ 30
Popular Question
to
PolenP
• 0
Recent Replies
Comment: limmaFit error when comparing TCGA RNA-Seq data
by
vernonlim98
• 0
Thanks for the advice. Am still new to RNA seq and R programming in general, and will just do the analysis by myself.
Answer: The Biostar Handbook. A bioinformatics e-book for beginners.
by
Istvan Albert
103k
Update as of **August 2025**: The book now includes a new online course: [**FastTrack Bioinformatics 2025**][course] at no extra cost. Bio…
Comment: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
by
GenoMax
154k
Likely because the SRA programs are doing database look ups as they retrieve the data where as with `curl` you are simply getting pre-exist…
Comment: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
by
Guilherme
• 0
That's a great tool! I wonder why downloading through curl via SRA's ftp is SO MUCH faster than through sra toolkit programs (fastq-dump or…
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere
by
GenoMax
154k
> they should align with common sequence at some ends, making one longer consensus sequence. You don't want to simulate reads like this.…
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere
by
cmdcolin
★ 4.3k
I believe the pairs will only have common sequence (e.g. the pairs will "overlap") if the insert size is small. the wgsim program has a fla…
Answer: X chromosome male and female imputation
by
barslmn
★ 2.4k
I think it's better to use the original 900 variants. If you have genotype information, you can get the fraction of heterozygous variants t…
Comment: Slam-Seq Conversion Rate per Read
by
michael.ante
★ 4.0k
Try to switch to percentage view of this graph. Stacked bar charts with different heights can sometimes be misleading.
Comment: Functional prediction for proteins of bacteria.
by
m90
▴ 30
Biochemical changes
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere
by
PolenP
• 0
Sorry about that. It's when I align the paired reads together like the left and righ, they should align with common sequence at some ends, …
Answer: Dictys refuses to use CUDA supported pytorch during installation
by
zwjiang
▴ 30
I fixed my problem by ``` conda create -y -p /project/spott/zwjiang/conda_envs/dictys_gpu -c conda-forge python=3.9 mamba conda activat…
Comment: HIV : gtf or gff annotation
by
Ales
▴ 50
Thank you for your response! We have just posted the full preprint to BioRxiv (https://www.biorxiv.org/content/10.1101/2025.09.24.675449v1)…
Comment: Does this adapter content from fastqc to warrant trimming prior to alignment?
by
curious
▴ 890
Just adding some detail here that may help draw some connections with other posts, I did a bunch of sleuthing with selectively trimming dif…
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere
by
cmdcolin
★ 4.3k
It's a little unclear what you mean by "I was able to use wgsim, but when I tried aligning the paired-reads, it's not aligning together."
Comment: using packages with conda
by
ATpoint
89k
Just to be sure: You ssh into a remote server, correct? Die you setup the conda environment on your local machine or the remote? Must be th…
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