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1,046 results • Page 3 of 21
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5
votes
4
replies
2.2k
views
How do we process Kallisto output (continuous real values) for DESEQ2 analysis (which strictly require discrete count values)?
read-counts DESEQ2 differential-gene-expression kallisto
updated 24 days ago by 43k • written 2.7 years ago by ▴ 170
5
votes
5
replies
568
views
NCBI MEGABLAST versus UCSC BLAT
blast blat alignment megablast
updated 24 days ago by ▴ 580 • written 25 days ago by ▴ 40
5
votes
4
replies
353
views
I'm new to cell ranger. Can single cells prepared with a protocol other than the 10x genomics protocol not be processed with cell ranger?
cellranger scRNA-seq 10x
18 days ago by Spring • 0
5
votes
13
replies
1.5k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 13 days ago by 82k • written 15 days ago by ★ 1.7k
5
votes
5
replies
247
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA DADA2 metabarcoding
updated 1 day ago by ▴ 30 • written 2 days ago by ▴ 150
5
votes
5
replies
875
views
Blacklist for bacterial genome [ChIPseq]?
ChIPseq Blacklist
updated 21 days ago by 43k • written 10 months ago by ▴ 30
5
votes
4
replies
681
views
How to compare the quality of assemblies
nextdenovo assembly hifiasm pacbio
10 days ago by kirillkirilenko ▴ 40
5
votes
2
replies
1.8k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq batch batch-effect sequencing
updated 17 days ago by 43k • written 3.0 years ago by ▴ 60
5
votes
3
replies
733
views
Illumina reads preprocessing best practice for snp calling applications
Illumina snp
updated 14 days ago by • 0 • written 9 months ago by ▴ 310
5
votes
5
replies
555
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 17 hours ago by • 0 • written 9 days ago by ★ 3.9k
5
votes
4
replies
365
views
Forum: Ideal PC configurations and operating system for bioinformatics laboratory
PC
1 day ago by Estevão • 0
5
votes
6
replies
7.3k
views
scatter plot, aov()
aov scatter-plot anova
updated 17 days ago by 43k • written 3.2 years ago by ▴ 170
5
votes
3
replies
410
views
Ensembl assembly choice for DNA reference with no combined primary assembly
alignment HISAT2 RNA-Seq ensembl Assembly
updated 22 days ago by 142k • written 22 days ago by ▴ 20
5
votes
2
replies
1.0k
views
How to perform batch correction when we have only single condition?
sva combat batch-effect DESeq2
updated 17 days ago by 43k • written 3.8 years ago by ▴ 680
5
votes
14
replies
1.0k
views
Not getting any modification calls in nanopore reads with dorado basecaller
mofications dorado basecalling nanopore methylation
updated 23 days ago by 142k • written 6 weeks ago by ▴ 20
5
votes
4
replies
2.8k
views
genefu for PAM50 prediction
RNA-Seq breast cancer subtyping
updated 17 days ago by ▴ 70 • written 5.7 years ago by ▴ 50
5
votes
4
replies
683
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq EdgeR DEGs DESeq2
15 days ago by BioinfGuru ★ 1.7k
5
votes
20
replies
4.2k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression RNA-seq
updated 24 days ago by 43k • written 6.2 years ago by ▴ 90
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression RNA-seq gene-ontology
updated 24 days ago by 43k • written 6.5 years ago by ★ 1.6k
5
votes
6
replies
510
views
Programmatically retrieving positions of protein active site residues
Uniprot PDB Proteins
updated 3 days ago by ▴ 760 • written 4 days ago by ▴ 40
4
votes
6
replies
493
views
Odd results with BLAST remote
blast remote NCBI
updated 18 days ago by ▴ 180 • written 19 days ago by ▴ 150
4
votes
7
replies
584
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
4 days ago by e.r.zakiev ▴ 210
4
votes
6
replies
3.8k
views
Taking the difference of two VCFs (or removing singletons)
genome sequencing singleton SNP filter
updated 4 days ago by ▴ 20 • written 9.6 years ago by ▴ 40
4
votes
5
replies
548
views
Getting refseq assembly accession numbers from list of species names
haystac accession refseq assembly ncbi
updated 29 days ago by 142k • written 29 days ago by • 0
4
votes
3
replies
367
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc conda nextflow
updated 6 days ago by 3.2k • written 7 days ago by ▴ 40
4
votes
3
replies
10k
views
short and long reads
long-reads Assembly short-reads
updated 28 days ago by 43k • written 10.0 years ago by ▴ 290
4
votes
4
replies
441
views
How do I install plink2 on a mac?
plink2 plink
updated 19 days ago by 11k • written 21 days ago by ▴ 10
4
votes
15
replies
1.6k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR DESeq Differential-Expression RNA-Seq
updated 9 hours ago by ★ 7.1k • written 4 months ago by ▴ 10
4
votes
6
replies
1.5k
views
CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRleFromGR(x, weight = weight, ignore.strand = ignore.strand): Seqlength…
gff3 GenomicRanges ORFik GenomicFeatures
updated 19 days ago by 142k • written 15 months ago by ▴ 30
4
votes
2
replies
397
views
Missing protein (VEGF-A) in String db
VGFA stringdb
updated 8 days ago by • 0 • written 12 weeks ago by ▴ 20
4
votes
6
replies
3.9k
views
Correcting for batch effect in RNA-seq data
RNA-Seq batch-effect
updated 16 days ago by 43k • written 4.8 years ago by ▴ 30
4
votes
0
replies
132
views
Herald: The Biostar Herald for Monday, April 29, 2024
herald
5 days ago by Biostar 2.7k
4
votes
4
replies
352
views
How to fetch published paper of a BioProject
BioProject pumbed NGS
24 days ago by Morteza • 0
4
votes
4
replies
14k
views
Heatmap with custom gene labels annotated on the rows
differential-gene-expression RNAseq heatmap
updated 24 days ago by 43k • written 4.7 years ago by ▴ 370
4
votes
2
replies
1.8k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF SAM BAM GFF minimap2
updated 17 days ago by ▴ 130 • written 12 months ago by • 0
4
votes
5
replies
3.4k
views
Please clarify me about countOverlaps()?
RNA-Seq countOverlaps R
updated 17 days ago by 43k • written 6.3 years ago by ★ 1.9k
4
votes
4
replies
387
views
Bowtie2 mapping is slow
metagenomics bowtie2 mapping read
updated 22 days ago by 6.4k • written 4 weeks ago by • 0
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference 38build impute imputation
4 days ago by anna ▴ 20
4
votes
9
replies
2.7k
views
Tool: CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.3 years ago by • 0
4
votes
2
replies
3.8k
views
DESeq2 design and batch effect
RNA-Seq batch-effect DESeq2 Salmon
updated 15 days ago by 43k • written 6.5 years ago by ▴ 30
4
votes
2
replies
247
views
Trying to write bwa mem -> samtools view -> samtools sort loop
bwa samtools mapping genome
updated 29 days ago by 161k • written 29 days ago by • 0
4
votes
2
replies
304
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma voom R
4 days ago by pairedttest ▴ 10
4
votes
2
replies
321
views
Forum: Bioinformatics: Where do I start
Sequencing
updated 17 days ago by 43k • written 18 days ago by ▴ 10
4
votes
2
replies
349
views
Assume "yes" as the answer to any prompts with bioconda
docker container bioconda
updated 16 days ago by 8.6k • written 16 days ago by ▴ 20
4
votes
7
replies
506
views
To get p-values for the TPM
P-value TPM RSEM
updated 9 days ago by ★ 6.0k • written 10 days ago by • 0
4
votes
7
replies
589
views
DESeq2 Multifactor Design
RNA-seq DESeq2
updated 20 days ago by 43k • written 21 days ago by ▴ 20
4
votes
2
replies
1.2k
views
Tool: Introducing Cramino: a *fast* QC tool for long reads
long-read nanopore pacbio
updated 28 days ago by 43k • written 18 months ago by 47k
4
votes
11
replies
809
views
Redirection of Duplicate PMIDs
pubmed pmid
updated 10 days ago by 4.2k • written 11 days ago by • 0
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect DESeq2 combat_seq
updated 25 days ago by 43k • written 3.7 years ago by ▴ 20
4
votes
3
replies
7.6k
views
Genotype representation with 0, 1, 2 - what do they mean?
genotype representation phasing imputation gwas
updated 29 days ago by • 0 • written 5.9 years ago by ▴ 180
1,046 results • Page 3 of 21
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Recent Replies
Comment: creating batch colum for batch correction by ATpoint 82k
Not sure I follow. Can you first of all describe which comparisons you want to make, pretending there was no batch effect at all. Write dow…
Comment: Pindel Segmentation Fault Error by Ruqaiya • 0
This the tool still problematic?
Comment: Segmentation error while using a tool by Ruqaiya • 0
Thank you for the advice, i'll keep that in mind.
Comment: Segmentation error while using a tool by Ruqaiya • 0
I am trying to reproduce some bioinformatics data from a research paper-[this paper][1] as i was asked to work on an MRSA bioinfo project, …
Answer: Segmentation error while using a tool by Mensur Dlakic ★ 27k
Most likely you didn't do anything wrong. Going by your previous post that you have only 8 GB of RAM, the most likely reason is the lack of…
Comment: Segmentation error while using a tool by Thanujay S • 0
Hey @Ruqaiya! Can you please give more details on why smalt is opted here? According to what I can see, the tool has become obsolete! Why …
Comment: Extracting mutation status from MAF files - TCGA by Thanujay S • 0
Hey! Can you explain the question further? What have you tried?
Comment: Downloading older version of a tool by Ruqaiya • 0
I tried the 2nd option only. I got the files of older version from the author but that version isn't working on my WSL, it's showing Segmen…
Comment: filtering before dada2 by GenoMax 142k
> I encountered a significant decrease in the percentage of merged reads. You can check with `bbmerge.sh` from BBMap suite to see how many…
Comment: HCL database download by GenoMax 142k
Isn't the download link available above the plot: http://bis.zju.edu.cn/HCL/data/DGE/Adult-Transverse-Colon1_dge.txt.gz
Comment: fastq screen aligner no specified. by GenoMax 142k
You need to change this configuration file to point it to the location where the aligner executable can be found. So as an example followi…
Answer: Design matrix Differential expression analysis by Gordon Smyth ★ 7.1k
The expression levels do not change but the way that you have parametrized the expression levels does change. The two design matrices give…
Comment: The GDC Legacy Archive is retiring soon. by lcordeiro ▴ 40
Hi Zhenyu, do you happen to know how I can download metadata for some of the legacy files? I downloaded several IDATs from the legacy data …
Answer: Force PLINK2 to neglect chrX as the sex chromosome by chrchang523 10k
(cross-posted from https://groups.google.com/g/plink2-users/c/Qphx_6BpPII ) You need to use --chr-set, not --allow-extra-chr, to specify…
Answer: Easy way to find out which allele is minor allele from bed file? by chrchang523 10k
This question does not make sense. If you care about allele-order "information [being] lost in downstream applications", REF/ALT is the ob…
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