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121,953 results • Page
159 of 2440
Sort: Rank
Rank
Views
Votes
Replies
2
votes
7
replies
3.0k
views
Downstream analysis from STAR Alignment at transcript level
star
IsoformSwitchAnalyzeR
Transcript-level
deseq2
salmon
updated 4 months ago by
Zhihao
• 0 • written 20 months ago by
bassanio
▴ 70
0
votes
0
replies
643
views
trying to upgrade from Bio.pairwise2.align to Bio.Align
pairwise2
Bio.align
python
biopython
updated 20 months ago by
Ram
45k • written 20 months ago by
Richard
• 0
0
votes
4
replies
920
views
Values EXCEEDS the original data range after batch effect correction.
Batch-effect
Limma
updated 20 months ago by
Ram
45k • written 20 months ago by
Mary
• 0
3
votes
3
replies
810
views
learning bioinformatics
course
learning
updated 20 months ago by
Ram
45k • written 20 months ago by
sevda
• 0
0
votes
8
replies
1.7k
views
Phobius error: Could not read provided fasta sequence at phobius.pl line 408
Phobius
updated 19 months ago by
ido.idobar
▴ 10 • written 20 months ago by
Elizabeth
▴ 40
0
votes
0
replies
643
views
Understanding Homer output for makeTagDirectory
chip-seq
peaks
homer
makeTagDirectory
20 months ago by
Assa Yeroslaviz
★ 1.9k
1
vote
2
replies
1.5k
views
Create Signature Matrix Cibersort
Cibersort
20 months ago by
Nona
▴ 90
3
votes
0
replies
969
views
Herald:
The Biostar Herald for Monday, January 22, 2024
herald
20 months ago by
Biostar
3.6k
10
votes
4
replies
1.6k
views
Lollipop plot for genome-view genes and differential expressing visuallization
R
DEseq2
ggplot2
20 months ago by
Yao
▴ 30
21
votes
11
replies
2.4k
views
Forum:
How to overcome the imposter syndrome in bioinformatics?
advice
20 months ago by
sil_bioinfo
▴ 60
0
votes
0
replies
456
views
News:
Online course - Sex Chromosome Evolution
Evolution
Genomics
Sex-Chromosome
updated 20 months ago by
Ram
45k • written 20 months ago by
Physalia-courses
★ 2.6k
2
votes
3
replies
1.6k
views
How can we explain a lower reference allele frequency than alternative allele in large populations for some SNPs?
mutation
human-genome
SNP
updated 20 months ago by
Ram
45k • written 20 months ago by
m.koohi.m
▴ 120
1
vote
7
replies
2.3k
views
Problem with DRAGEN RNAseq hashtable directory
dragen
hashtable
llumina
RNA-seq
updated 20 months ago by
DBScan
▴ 530 • written 20 months ago by
yussab
▴ 100
0
votes
3
replies
886
views
LD store2 cannot be matched
FINEMAP
LDstore2
20 months ago by
peggy
• 0
0
votes
0
replies
551
views
KEGG orthology ID to E. coli gene symbol
symbol
KEGG
convert
20 months ago by
sooni
▴ 20
3
votes
4
replies
1.3k
views
split sequences into their codons in a table
R
fasta
codon-table
20 months ago by
Assa Yeroslaviz
★ 1.9k
3
votes
2
replies
839
views
Illumina reads to be processed and prepared for reference genome alignment
genome
alignment
trimming
next-gen
Illumina
updated 20 months ago by
shelkmike
★ 1.8k • written 20 months ago by
Veselina
• 0
1
vote
0
replies
522
views
DESeq2 contrasts and design formula for 2 conditions and 3 exposure times
DESeq2
DEG
updated 20 months ago by
Ram
45k • written 20 months ago by
pcar
▴ 10
0
votes
0
replies
435
views
Merging alignment graphs vs merging BAMs
bam
vg
20 months ago by
Daniel
• 0
0
votes
0
replies
910
views
Is there a RSeQC manual or guide
RSeQC
RNA
20 months ago by
gallardodiazmiriam
▴ 20
1
vote
2
replies
814
views
Gene Ontonology analysis of DEGs from rice genome
Gene-Ontology
Rice
Genome-annotation
20 months ago by
prity6459
• 0
28
votes
11
replies
37k
views
10 follow
Samtools View: Only Forward Or Reverse Strand
samtools
strand
updated 20 months ago by
shaoqian ma
• 0 • written 13.9 years ago by
Gregor Rot
▴ 550
0
votes
0
replies
639
views
What does ANOVA test over CoxPH model mean?
SurvivalAnalysis
CoxPH
ANOVA
Survival
20 months ago by
Manuel Sokolov Ravasqueira
▴ 110
0
votes
4
replies
989
views
Retrieving matched search terms when using NCBI's API
NCBI
API
20 months ago by
langziv
▴ 70
1
vote
2
replies
1.0k
views
Problem interpreting 'Per base sequence quality' report
galaxy
fastqc
20 months ago by
Sanjukta
• 0
4
votes
3
replies
1.0k
views
Is it possible to bulk-download gene expression + methylation data for a specific copy number loss on TCGA?
tcga
updated 20 months ago by
Zhenyu Zhang
★ 1.3k • written 20 months ago by
Pratik
★ 1.1k
0
votes
0
replies
476
views
Pathview modifies LFC genes. Is this normal?
gage
pathview
KEGG
R
20 months ago by
Alex
• 0
0
votes
2
replies
1.5k
views
invalid deflate data (invalid code lengths set)
Paired-End
Trimming
Fastq
TrimGalore
updated 20 months ago by
Ram
45k • written 20 months ago by
leonmcswain
▴ 10
0
votes
1
reply
776
views
Monotonic genes in results of differential gene expression analysis
differential-expression
RNA-seq
monotonic-genes
updated 17 months ago by
Ram
45k • written 20 months ago by
Shaimaa Gamal
▴ 10
1
vote
5
replies
1.7k
views
sam file error
samtools
20 months ago by
Chironex
▴ 50
1
vote
4
replies
940
views
How to quantify the correlation of variants between cells?
variant
20 months ago by
zau saa
▴ 150
0
votes
0
replies
754
views
gnomad api
gnomad
updated 20 months ago by
Ram
45k • written 20 months ago by
sushma
▴ 10
0
votes
0
replies
672
views
Downsampling or not in single cell RNA Seq Experiments
scRNA
Seq
Downsampling
Seurat
20 months ago by
MolGeek
▴ 80
0
votes
1
reply
827
views
How to split alignment into smaller chunks with node range
vg
updated 20 months ago by
Jordan M Eizenga
▴ 760 • written 20 months ago by
Wenhai
• 0
1
vote
5
replies
13k
views
fasterq-dump quit with error code 3
sratoolkits
sratools
dump
fasterq
fastq-dump
updated 20 months ago by
gernophil
▴ 130 • written 3.0 years ago by
Maliha
▴ 30
2
votes
1
reply
724
views
will the features.tsv file from 10X chromium be same for all donor individuals?
scRNA-seq
chromium
10x
single-cell
updated 20 months ago by
Ram
45k • written 20 months ago by
kousi31
▴ 100
1
vote
2
replies
896
views
Having trouble using the create-profmark tool in the HMMER suite
HMMER
create-profmark
20 months ago by
Jacob
• 0
0
votes
3
replies
2.1k
views
How to interpreting that ORA and GSEA results?
pathway
gsea
ora
updated 20 months ago by
Istvan Albert
103k • written 20 months ago by
ubuntubak
• 0
0
votes
0
replies
542
views
How do I export Plink files .dosage and .fam to R?
plink
20 months ago by
Travis
▴ 20
3
votes
7
replies
2.2k
views
Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set?
cell-barcode
MGI
DNBelab
single-cell
updated 14 months ago by
GenoMax
154k • written 20 months ago by
benjamin.pyenson
• 0
4
votes
8
replies
2.1k
views
Isolating and extracting regions in VCF file
ANNOVAR
vcftools
bcftools
GATK
VCF
updated 20 months ago by
Jeremy Leipzig
23k • written 20 months ago by
iarmir
▴ 10
7
votes
6
replies
7.7k
views
The purpose of scaling to a negative binomial distribution in single cell RNA-seq
RNA-Seq
scRNA-Seq
updated 20 months ago by
Ram
45k • written 7.5 years ago by
ericvaughn11
▴ 10
0
votes
1
reply
657
views
Question to order chr positions
GWAS
chromosomes
updated 20 months ago by
Ram
45k • written 20 months ago by
alex.sanchez
• 0
0
votes
3
replies
1.1k
views
Low featureCounts assigned rate
featureCounts
RNA-seq
hisat2
updated 20 months ago by
GenoMax
154k • written 20 months ago by
weather
• 0
2
votes
4
replies
1.9k
views
How to produce "publication quality figures" for MAGs from environmental samples, and visualize functional annotation results?
figures
visualization
publication
updated 20 months ago by
young_bioinformatician
▴ 240 • written 21 months ago by
jway
• 0
1
vote
3
replies
1.1k
views
How to check a specific gene level in a specific genus?
microbiome
updated 20 months ago by
inedraylig
▴ 70 • written 20 months ago by
sooni
▴ 20
1
vote
0
replies
719
views
Job:
Researcher/Postdoc to enhance computational resources for regulatory genomics with deep learning
deep-learning
updated 20 months ago by
Ram
45k • written 20 months ago by
Anthony Mathelier
▴ 910
0
votes
0
replies
384
views
Mutual information method for gene markers identification ???
scRNA-seq
mutual-information
updated 20 months ago by
Ram
45k • written 20 months ago by
Ondina
▴ 100
3
votes
4
replies
1.5k
views
Find reference fasta based on M5/MD5 string
reference
fasta
20 months ago by
WouterDeCoster
48k
4
votes
1
reply
704
views
How to learn transcriptomics in R
R
Transcriptomics
updated 20 months ago by
Matthias Zepper
5.1k • written 20 months ago by
noahbudd02
▴ 10
121,953 results • Page
159 of 2440
Recent Votes
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
Answer: MAPQ algorithms of Giraffe
Answer: MAPQ algorithms of Giraffe
Answer: Illumina Instrument Type from fastq?
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Recent Awards •
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Teacher
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colindaven
8.0k
Popular Question
to
m90
▴ 30
Popular Question
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PolenP
• 0
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xiaoleiusc
▴ 140
Teacher
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cfos4698
★ 1.2k
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sacha
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istdasklar
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Recent Replies
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…
Answer: pySCENIC aucell matrix is all 0s
by
Tripfantasy
• 0
Sorry to those of you having the same issue. I haven't been on here in quite some time! I've documented my fix on pySCENIC's github page be…
Comment: [vg giraffe] Unable to add read group to BAM file
by
anovak
▴ 180
I think this is still not quite right because I think your tags need to be tab-separated in the output to really be parseable, and here the…
Answer: MAPQ algorithms of Giraffe
by
anovak
▴ 180
`vg giraffe` does not use the exact same MAPQ algorithm as bwa-mem. However, its mapping qualities are still meant to be Phred-scale probab…
Comment: using packages with conda
by
raquel
• 0
Yes, I'm using SSH session
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere
by
Mensur Dlakic
★ 30k
I think only a fraction of sequencing errors can be specified. If a mix of a reference and a mutated genome is included, setting sequencing…
Comment: using packages with conda
by
ATpoint
89k
Cannot reproduce. Is this run via some sort of server/HPC/scheduler/something?
Comment: limmaFit error when comparing TCGA RNA-Seq data
by
ATpoint
89k
Seriously, an ordinary limma-voom analysis between two groups is as little of 5 lines of code. Please read the limma user guide which cover…
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