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694
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Issue with bigWigSummary utility of Kent/UCSC utilities
bigWig UCSC
updated 18 months ago by 166k • written 18 months ago by • 0
1
vote
3
replies
1.1k
views
'incomplete' intersect among two files
bedtools bed intersect
18 months ago by Lila M ★ 1.3k
0
votes
1
reply
748
views
deepTools computeMatrix output import into R for enrichment calculations
R deeptools computeMatrix deepTools
updated 18 months ago by 166k • written 18 months ago by • 0
1
vote
2
replies
1.0k
views
BAM to CRAM and BAM recover with smaller size
BAM samtools CRAM
updated 18 months ago by ★ 1.3k • written 18 months ago by ▴ 400
0
votes
0
replies
409
views
admixfrog for high-coverage data
introgression
18 months ago by gubrins ▴ 350
0
votes
5
replies
1.7k
views
VCF file not being indexed, decided to sort could not sort
bcftools
updated 18 months ago by 5.1k • written 18 months ago by • 0
1
vote
2
replies
1.7k
views
How to Modify Reference Sequence and Annotation Files
reference edit annotation
updated 18 months ago by • 0 • written 3.5 years ago by ▴ 340
2
votes
3
replies
1.0k
views
representing PCs as marginal distribution on x and Y acis
PCAtool Deseq2 Pcaplot PCA
updated 18 months ago by ★ 3.1k • written 18 months ago by • 0
0
votes
3
replies
1.4k
views
Calculation of λ1000 for a continuous trait
SNP GWAS inflation
18 months ago by Apprentice ▴ 190
3
votes
2
replies
921
views
With DESeq2 "Not full rank" Error with design
DESeq2
18 months ago by feather-W • 0
1
vote
1
reply
588
views
Seeking Advice on Pre-processing Single Cell Data for Gene Mapping
single analysis cell preprocessing
updated 18 months ago by 154k • written 18 months ago by ▴ 10
0
votes
1
reply
1.2k
views
updateR() error
R update
updated 18 months ago by ★ 3.1k • written 18 months ago by ▴ 180
0
votes
0
replies
416
views
Haplotype Phasing from Yeast strains
yeast haplotype phasing
18 months ago by Sven K • 0
1
vote
3
replies
912
views
Can't use VarScan2 to call somatic variants from my tumor/sample vcf pair
mutations vcf somatic varscan2 samtools
updated 18 months ago by 166k • written 18 months ago by ▴ 20
0
votes
0
replies
394
views
cufflinks- cuffquant issue
cufflinks
18 months ago by soyeon • 0
2
votes
2
replies
846
views
compare dimplot(single cell)
DEG scRNAseq
18 months ago by kayah ▴ 20
0
votes
1
reply
625
views
Edit erroneous line using bcftools
awk vcf grep bcftools
updated 18 months ago by 154k • written 18 months ago by • 0
0
votes
0
replies
536
views
News: Online course on Genome Assembly and Annotation (1 seat left)
Galaxy GenomeAssembly GenomeAnnotation
18 months ago by Physalia-courses ★ 2.6k
4
votes
1
reply
728
views
Doplot to display 2 metadata variables
single-cell seurat analysis dotpolot
updated 18 months ago by ★ 1.7k • written 18 months ago by ▴ 10
1
vote
1
reply
652
views
--busco_db and --busco_seed_species with RNA-seq
RNA-seq Funannotate busco
18 months ago by san96 ▴ 190
1
vote
3
replies
1.3k
views
Forum: Development plan for a bioinformatics database developer/coder
developer
18 months ago by pixie@bioinfo ★ 1.5k
3
votes
3
replies
1.7k
views
Strandness of Isoseq HiFi reads?
minimap2 pacbio isoseq
updated 18 months ago by ▴ 40 • written 3.5 years ago by ▴ 140
0
votes
0
replies
554
views
Computational Package to engage Type 2 Diabetes Knowledge Portal (T2DKP)
workflow Package
18 months ago by Shicheng Guo ★ 9.6k
1
vote
3
replies
1.3k
views
Mathematical/Statistical models to predict mRNA half-life
mRNA half-life
updated 18 months ago by 22k • written 18 months ago by ★ 9.6k
1
vote
1
reply
748
views
Demultiplexing scRNAseq data using popscle
segmentation-fault Demultiplex popscle
18 months ago by valentinapazom ▴ 10
7
votes
8
replies
6.4k
views
Forum: Bioinformatics career transition
career forum
updated 18 months ago by ★ 19k • written 18 months ago by ▴ 20
1
vote
5
replies
3.0k
views
Single cell demultiplexing using 10x and TotalSeq-B
demultiplexing cellranger antibodies single-cell
4 months ago by txema.heredia ▴ 250
0
votes
1
reply
673
views
Pathway activity in Bulk-RNA-SEQ analysis
R RNA-seq transcriptomics
updated 18 months ago by ★ 19k • written 18 months ago by ▴ 10
1
vote
2
replies
709
views
Error executing MEGAHIT
linux terminal megahit
updated 18 months ago by 154k • written 18 months ago by • 0
8
votes
5
replies
2.5k
views
Overriding a color palette in R to emphasize specific data points
R ggplot2
updated 18 months ago by 15k • written 18 months ago by ▴ 10
1
vote
8
replies
2.6k
views
6 follow
Using aspera-connect to UPLOAD fastq files to ENA on Linux
ENA aspera-connect ascp
updated 18 months ago by • 0 • written 18 months ago by • 0
5
votes
2
replies
1.4k
views
Missing protein (VEGF-A) in String db
VGFA stringdb
updated 17 months ago by ▴ 10 • written 19 months ago by ▴ 20
1
vote
0
replies
482
views
News: NCBI's ClinVar now accepting somatic variation data
variation NCBI somatic-variants ClinVar
18 months ago by PeterC_NCBI ▴ 520
2
votes
5
replies
2.7k
views
implementation of k-mer counting from krakenuniq to kraken2
metagenomics kraken2 kraken krakenuniq classification
updated 18 months ago by 35k • written 2.6 years ago by ▴ 10
0
votes
2
replies
1.5k
views
converting VCF files to TSV file
vcfmutations variantcellformat
updated 18 months ago by ▴ 490 • written 18 months ago by • 0
2
votes
1
reply
582
views
lncRNA and ncPEPs identification
lncRNA
updated 18 months ago by • 0 • written 18 months ago by ▴ 40
0
votes
0
replies
442
views
Music2 human to mouse deconvolution
deconvolution liftover music2
18 months ago by rbronste ▴ 420
0
votes
2
replies
892
views
Weird Basecalled reads PHRED quality plot from pycoQC
pycoQC nanopore sequencing
18 months ago by njornet ▴ 20
0
votes
0
replies
493
views
computeGCBias outputs
GC bam deepTools GCbias
18 months ago by pablo ▴ 350
3
votes
10
replies
2.1k
views
Intersect gene IDs list and GFF3 to get the annotation.
annotation GFF
18 months ago by Lissa Cruz Saavedra • 0
0
votes
0
replies
393
views
Pindel zygosity determination
depth vaf pindel Zygosity
18 months ago by arya.sagittarius ▴ 10
1
vote
3
replies
1.1k
views
How to predict the affinity between Protein and RNA?
Protein-RNAinteractions prediction deeplearning
updated 18 months ago by ★ 3.1k • written 18 months ago by • 0
3
votes
3
replies
1.9k
views
Snakemake's SyntaxError positional argument follows keyword argument
snakemake
updated 18 months ago by 15k • written 18 months ago by ▴ 10
2
votes
2
replies
1.1k
views
Seeking Help with Cell Ranger Multi Error in fixed-RNA-profiling
chromium fixed-RNA-profiling cellranger
updated 18 months ago by • 0 • written 18 months ago by ▴ 10
1
vote
3
replies
877
views
ONT methylation data background noise
data noise
updated 14 months ago by 8.0k • written 18 months ago by ▴ 180
7
votes
8
replies
3.8k
views
Create Conda Environment with YAML File
Python
updated 18 months ago by ★ 3.1k • written 18 months ago by ▴ 110
6
votes
3
replies
3.0k
views
ChipQC doesn't run
ChIP-Seq
updated 18 months ago by • 0 • written 5.6 years ago by ▴ 160
1
vote
4
replies
2.3k
views
gnomAD4.0 Hail Table Downloading
NGS gnomAD
updated 18 months ago by ▴ 530 • written 22 months ago by ▴ 60
4
votes
6
replies
995
views
Protein loops
protein Loop
18 months ago by Curious ▴ 10
3
votes
8
replies
8.1k
views
6 follow
Download CAZy database
genome gene database cazy
updated 18 months ago by 154k • written 7.6 years ago by ▴ 190
121,938 results • Page 136 of 2439
Recent Votes
C: Filtering low variance genes for WGCNA
A: How to normalize my rna seq data?
Answer: Linear regression vs DESeq2 models for DEG analysis
Answer: Linear regression vs DESeq2 models for DEG analysis
Answer: Linear regression vs DESeq2 models for DEG analysis
Answer: Linear regression vs DESeq2 models for DEG analysis
Answer: Linear regression vs DESeq2 models for DEG analysis
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Recent Replies
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 15k
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…
Comment: real time PCR data analysis by ATpoint 89k
I cannot guide on GraphPad. It's commercial software so better contact their support.
Answer: Linear regression vs DESeq2 models for DEG analysis by swbarnes2 15k
DE genes in bulk RNASeq is what DESeq2 was made for, so why wouldn't you use it? RPKM is not an appropriate normalization method here. M…
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