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121,940 results • Page
141 of 2439
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Votes
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0
votes
6
replies
1.2k
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Contamination in my FASTQC files
Fastqc
bowtie2
19 months ago by
carlosgonzalezcruz327
▴ 20
0
votes
0
replies
860
views
Job:
Assistant professor in Computational biology with a focus on machine learning for multimodal molecular biology data
Multiomics
Machine-Learning
19 months ago by
lukas.kall
▴ 40
1
vote
2
replies
1.5k
views
Nextflow crash on AWS Batch with transition error
BWA
Nextflow
AWS
updated 19 months ago by
barslmn
★ 2.4k • written 19 months ago by
hkarakurt
▴ 200
1
vote
4
replies
1.0k
views
Estimate cell label fitness in a clustering
single-cell
cell-type
updated 19 months ago by
LChart
5.1k • written 19 months ago by
roussine
▴ 10
0
votes
0
replies
556
views
Calculate PSI values for pre-called splicing events in GFF from new fastq files
alternative
spladder
PSI
splicing
19 months ago by
sckinta
▴ 740
1
vote
2
replies
2.9k
views
Filter out doublet and Clustering
single-cell
updated 19 months ago by
jv
★ 1.9k • written 22 months ago by
synat.keam
▴ 120
4
votes
9
replies
1.9k
views
Max length reads from fastq
fastq
updated 19 months ago by
Michael
56k • written 19 months ago by
marco.barr
▴ 180
17
votes
34
replies
21k
views
10 follow
Issues installing bcl2fastq?
bcl2fastq
demultiplexing
updated 19 months ago by
barslmn
★ 2.4k • written 8.1 years ago by
a.rex
▴ 350
0
votes
0
replies
639
views
Annotation transfer between QuPath (H&E) and 10X spatial transcriptomics Visium
alignment
seurat
spaceranger
visium
19 months ago by
Nicolas Rosewick
11k
6
votes
8
replies
2.7k
views
Difference between GLM and Wilcoxon rank sum test
GLM
rank-sum
Wilcoxon
19 months ago by
yxwucq
• 0
0
votes
0
replies
386
views
A way to read both the DNA fragment and the nascent RNA
ChRO-seq
RNA
transcription
NET-seq
nascent
19 months ago by
Chris
• 0
0
votes
1
reply
866
views
seaborn dispersion graph
graph
dispersion
seaborn
updated 19 months ago by
Shred
★ 1.6k • written 19 months ago by
brunofelicianodeomena
• 0
1
vote
5
replies
1.1k
views
How to normalise RNA seq data from two independent experiments to the same scale.
RNAseq
updated 19 months ago by
jv
★ 1.9k • written 19 months ago by
Mo
▴ 50
0
votes
0
replies
414
views
Get metadat from the ICGC data portal
hg38
ICGC
Cancer
19 months ago by
elisheva
▴ 120
0
votes
1
reply
557
views
Pileup of mapped diploid
diploid
Pileup
19 months ago by
Axzd
▴ 80
1
vote
1
reply
658
views
Testing the effect of the salinity water on abundance estimates
Salinity
updated 19 months ago by
ATpoint
89k • written 19 months ago by
Thibaut
▴ 10
0
votes
6
replies
1.5k
views
How can I see probe IDs in a microarray?
R
microarray
probe
Affymetrix
19 months ago by
wyt1995
▴ 40
0
votes
1
reply
705
views
Whole genome assembly
genome-assembly
updated 19 months ago by
Ram
45k • written 19 months ago by
manaswiniparija3
▴ 60
1
vote
1
reply
543
views
Fish_genome_assembly
bgseq
Longreads
oxfordnanopre
hybridassembly
updated 19 months ago by
dthorbur
★ 3.1k • written 19 months ago by
manaswiniparija3
▴ 60
0
votes
0
replies
511
views
Annotating Seurat samples when merging objects
single
Seurat
cell
rnaseq
19 months ago by
Gerard
▴ 20
1
vote
0
replies
596
views
News:
shournal: A Tool for Bioinformaticians to Boost Research Reproducibility
reproducability
terminal
bash
19 months ago by
David Langenberger
11k
0
votes
6
replies
1.7k
views
Rooting phylogenetic trees in R using Treeio's root function: Trees don't seem to root.
R
MrBayes
19 months ago by
lingxue
• 0
1
vote
4
replies
1.0k
views
Differential analysis using R
DNA
methylation
updated 19 months ago by
Michael
56k • written 19 months ago by
maryak
▴ 20
1
vote
1
reply
601
views
How to determine if a somatic mutation alters transcription factor binding site?
cancer
motif
TFBS
somatic-mutation
updated 19 months ago by
Ram
45k • written 19 months ago by
ConvolutedGenome
▴ 60
0
votes
1
reply
605
views
Protein protein interaction network
interaction
protein
network
updated 19 months ago by
dthorbur
★ 3.1k • written 19 months ago by
Tomk
• 0
0
votes
7
replies
1.2k
views
Error "ckalloc: request for negative space" about multiz
multiz
19 months ago by
marh32
• 0
3
votes
3
replies
1.2k
views
How to analyze DEGs in scRNA-seq data?
DEG
single-cell
scRNA-seq
rna-seq
updated 19 months ago by
Ram
45k • written 19 months ago by
kayah
▴ 20
5
votes
4
replies
2.9k
views
How to call mitochondrial SNP?
SNP
mitochondrial
updated 19 months ago by
Ram
45k • written 8.4 years ago by
hxlei613
▴ 100
0
votes
2
replies
1.6k
views
GATK's new best practice for mitochondrial variant calling
SNP
sequencing
updated 19 months ago by
sriram_pharm
• 0 • written 5.5 years ago by
lovelysunzt
• 0
1
vote
2
replies
1.0k
views
scRNAseq output generated using STARsolo has gene_id rather than gene_name
STARsolo
RNAseq
Seurat
single-cell
19 months ago by
Lauren
• 0
0
votes
0
replies
375
views
Help plotting enrichment results - kegg terms
Enrichment-analysis
KEGG
updated 19 months ago by
Ram
45k • written 19 months ago by
DByter
• 0
0
votes
0
replies
361
views
DWGSIM incorrectly mapped reads
DWGSIM
RNA-seq
mapping
transcriptomics
19 months ago by
cst_rmrz
• 0
6
votes
6
replies
1.7k
views
Forum:
You have 3 days of zero obligations and expansive resources. What are you building?
hypothetical
thought-experiment
19 months ago by
jared.andrews07
★ 19k
1
vote
8
replies
2.1k
views
6 follow
Finding insert sequences using long reads
insert-sequences
Nanopore
long-read-assembly
updated 17 months ago by
Anand Rao
▴ 640 • written 19 months ago by
bvm
▴ 20
1
vote
2
replies
3.9k
views
Align dorado output to reference
minimap2
bam
nanopore
dorado
updated 19 months ago by
colindaven
8.0k • written 19 months ago by
njornet
▴ 20
0
votes
6
replies
1.3k
views
Odd behaviour - NCBI Eutils
NCBI
Eutils
esearch
Eutilities
efetch
updated 9 months ago by
GenoMax
154k • written 19 months ago by
npb27
▴ 20
0
votes
2
replies
786
views
DiffBind issue in identification of differentially enriched peaks between two conditions
DiffBind
ChIP-Seq
19 months ago by
accibio
▴ 20
1
vote
1
reply
621
views
News:
Integrated Genome Browser (IGB) Office Hours
Integrated-Genome-Browser
IGB
updated 19 months ago by
Ram
45k • written 19 months ago by
IGB Helper
• 0
0
votes
0
replies
310
views
Reactome isChimeric attribute
reactome
19 months ago by
Ana
▴ 20
0
votes
5
replies
1.3k
views
loop string set
python
stringset
updated 19 months ago by
rpolicastro
13k • written 19 months ago by
aj123
▴ 130
0
votes
0
replies
547
views
issue with the Arima genomics pipeline for Hi-C scaffolding
plant
pacbio
assembly
genome
Hi-C
19 months ago by
rj.rezwan
▴ 20
3
votes
1
reply
823
views
How to use `bai_file`/`sample_id` (cardinality=10) and `bin_id` (cardinality=2875) much efficiently here?
nextflow
19 months ago by
Đặng Hải Đăng
• 0
5
votes
3
replies
1.9k
views
samtools view: error reading file
samtools
bowtie2
updated 19 months ago by
bioinfo_ga
▴ 70 • written 19 months ago by
ray
• 0
4
votes
14
replies
7.8k
views
Trouble with bedtools getfasta
bedtools
getfasta
written 3.6 years ago by
gkunz
▴ 30
0
votes
0
replies
389
views
Interpret ImpulseDE2 output?
RNA-seq
19 months ago by
CTLong
▴ 140
1
vote
3
replies
944
views
RNA-seq bam file normalization
RNA-seq
bam
normalization
updated 19 months ago by
dsull
★ 7.7k • written 19 months ago by
maplewj
▴ 20
1
vote
1
reply
728
views
FeatureCounts has duplicate Gene names
RNA-seq
updated 19 months ago by
GenoMax
154k • written 19 months ago by
Confused_human
▴ 30
0
votes
0
replies
475
views
Tutorial for COSMIC? Any way to calculate VAF?
COSMIC
19 months ago by
gernophil
▴ 130
0
votes
0
replies
554
views
Forum:
What other data types and pipelines you would like to see from the Genomics Data Commons (GDC)
gdc
tcga
genomics-data-commons
updated 19 months ago by
Ram
45k • written 19 months ago by
Zhenyu Zhang
★ 1.3k
0
votes
0
replies
406
views
Characterization of mutations in vcf files
mutations
vcf
characterization
19 months ago by
RUBEM
• 0
121,940 results • Page
141 of 2439
Recent Votes
Comment: Help understanding this per base sequence content failure fastqc plot
Comment: Help understanding this per base sequence content failure fastqc plot
Answer: Linear regression vs DESeq2 models for DEG analysis
Comment: Linear regression vs DESeq2 models for DEG analysis
Comment: Looking to learn practical bioinformatics
Comment: Looking to learn practical bioinformatics
Comment: Linear regression vs DESeq2 models for DEG analysis
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i.sudbery
22k
Teacher
to
Istvan Albert
103k
Popular Question
to
saruman
▴ 10
Popular Question
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frarodmar17
• 0
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nuorain
▴ 40
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charms.charms
• 0
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Recent Replies
Answer: LASSO parameter selection: lambda min vs lambda 1se
by
Mensur Dlakic
★ 30k
You are asking us to help you justify something after the fact. You seem to have picked a course of action arbitrarily, though that does no…
Comment: Help understanding this per base sequence content failure fastqc plot
by
Mensur Dlakic
★ 30k
Make this an answer rather than comment?
Comment: Feasibility of detecting PCR-chimeric reads with Machine Learing (ML) for organe
by
andres.firrincieli
3.9k
While there is no specific rule against the use of ChatGPT or similar, this must be clearly stated in the answer
Comment: cellranger mkref fail/error
by
Arup Ghosh
3.4k
As you managed to run each organism separately successfully. Does the combined size of the FASTA files exceed the amount of memory you spec…
Comment: different methods target identification
by
ATpoint
89k
Oh come on... https://www.biostars.org/p/75548/ https://www.biostars.org/p/357878/
Answer: Feasibility of detecting PCR-chimeric reads with Machine Learing (ML) for organe
by
teamardigen
• 0
Your idea is definitely feasible on Illumina reads. Since curated chimera datasets are rare, most people simulate them in silico (concatena…
Comment: Linear regression vs DESeq2 models for DEG analysis
by
ATpoint
89k
+1 Your answer should be the top-voted answer in this thread https://www.biostars.org/p/284775/ as it actually addresses conceptual diffe…
Comment: Linear regression vs DESeq2 models for DEG analysis
by
swbarnes2
15k
It is not clear to me that you can meaningfully correct for 5 different batches with two samples a piece.
Comment: Does this adapter content from fastqc to warrant trimming prior to alignment?
by
GenoMax
154k
> I am not sure if there would be primer dimer sequences I should have said adapter dimers above. Correction made.
Comment: Help understanding this per base sequence content failure fastqc plot
by
lieven.sterck
16k
that 151st base added is a base to ignore (it's a kind of random addition) ... if I recall correctly it's a consequence of the technology. …
Comment: Linear regression vs DESeq2 models for DEG analysis
by
FioG
• 0
@swbarnes2 Thank you for your response! I am new to RNA seq analysis and was originally recommended to use the LM method following cqn and …
Comment: Does this adapter content from fastqc to warrant trimming prior to alignment?
by
curious
▴ 890
Thank you, the adapter sequences are specified as CTGTCTCTTATACACATCT+ATGTGTATAAGAGACA is the SampleSheet.csv file from the sequencing run.…
Comment: how to explain the sample size discrepancy in UCSC Xena
by
nuorain
▴ 40
Thank you very much.
Answer: how to explain the sample size discrepancy in UCSC Xena
by
i.sudbery
22k
Because there wasn't RNA-seq analysis performed for every sample in TCGA?
Answer: Linear regression vs DESeq2 models for DEG analysis
by
i.sudbery
22k
There are two main problems with using linear models for read-count based analyses. Firstly, linear models assume a normal distribution…
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