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1,066 results • Page 2 of 22
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8
votes
16
replies
931
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 6 days ago by ★ 2.4k • written 8 weeks ago by • 0
8
votes
12
replies
1.9k
views
Metric to use for RNAseq expression matrix
gene-expression TPM RNA-Seq counts batch-effect
14 days ago by Ram 43k
8
votes
10
replies
749
views
bash script
whole-genome-sequencing
updated 16 days ago by 43k • written 24 days ago by ▴ 30
8
votes
4
replies
3.0k
views
Read count correlation between samples
differential-gene-expression RNA-seq
updated 23 days ago by 43k • written 6.5 years ago by ★ 1.6k
8
votes
3
replies
373
views
How to extract rows with specific values in R for all the columns?
R
28 days ago by Lakshmi ▴ 20
8
votes
8
replies
623
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 7 days ago by 14k • written 8 days ago by ▴ 10
8
votes
6
replies
637
views
The bioinformatics paper reappears, but the results are significantly different from the original results
reproducibility
27 days ago by jiao ▴ 40
8
votes
2
replies
796
views
News: FINAL CALL - Single-Cell RNA-Seq Data Analysis: A Practical Introduction (May 6-8, 2024 in Berlin)
single-cell sequencing
27 days ago by David Langenberger 11k
8
votes
5
replies
5.6k
views
ISCN annotation for SV/CN VCF files
SV
written 8 months ago by ▴ 60
8
votes
12
replies
3.5k
views
Why should ATAC-seq mapped reads be shifted +4 and -5 for +strand and -strand, respectively
ATAC-seq
updated 29 days ago by • 0 • written 3.4 years ago by ▴ 40
8
votes
6
replies
2.5k
views
Batch effect removal with the help of sva
SVA batch-effect gene-expression
updated 24 days ago by 43k • written 3.5 years ago by ▴ 240
8
votes
6
replies
2.6k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 14 days ago by 3.0k • written 24 months ago by ▴ 230
7
votes
7
replies
1.1k
views
Prediction tools summary - zero values
statistics
updated 15 days ago by • 0 • written 6 months ago by ▴ 50
7
votes
4
replies
1.4k
views
Is there any journal article to reference removeBatchEffect function from Limma?
batch removebatcheffect limma rna-seq batch-effect
updated 15 days ago by 43k • written 21 months ago by ▴ 20
7
votes
7
replies
1.5k
views
Forum: Bioinformatician who was retaliated against after reporting discriminatory harassment - Please help me navigate getting out of the situation I'm in
Career advice
updated 17 days ago by ★ 2.5k • written 17 days ago by • 0
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq SNP
updated 7 days ago by ▴ 850 • written 6.1 years ago by ▴ 10
7
votes
3
replies
2.9k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
updated 13 days ago by 6.4k • written 16 months ago by ▴ 130
7
votes
4
replies
2.1k
views
filtering genes by pearson correlation
correlation RNA-Seq R
updated 15 days ago by 43k • written 6.1 years ago by ▴ 120
7
votes
3
replies
4.6k
views
how to deal with batch effect in TCGA RNA-seq dataset
TCGA RNA-Seq batch-effect
updated 14 days ago by 43k • written 5.1 years ago by ▴ 100
7
votes
3
replies
1.2k
views
biomaRt::getSequence - Invalid type argument
biomaRt R
updated 15 days ago by 43k • written 3.9 years ago by ▴ 680
7
votes
2
replies
284
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 8 days ago by ▴ 390 • written 10 days ago by • 0
7
votes
7
replies
588
views
Can you suggest a protein PDB that has two chainst but only 50 total number of atoms?
protein pdb protein-databank
updated 19 days ago by 4.6k • written 20 days ago by • 0
7
votes
6
replies
517
views
Filtering sam or bam file with maximum matching region
crisper-edited alignment match
11 days ago by analyst ▴ 30
7
votes
8
replies
680
views
Why are the basics so complicated? Basic coverage filtering for VCF files
filter vcf coverage
updated 20 days ago by ▴ 40 • written 23 days ago by ▴ 40
7
votes
8
replies
689
views
6 follow
How to BLAST more than 5 sequences against UniProt database?
BLAST Protein UniProt
27 days ago by Riq ▴ 50
7
votes
6
replies
1.3k
views
using different microarray datasets (meta-analysis?) for DEG pipeline
microarray meta-analysis DEG batch-effect
updated 14 days ago by 43k • written 4.9 years ago by ▴ 30
7
votes
2
replies
3.7k
views
Timeout on getBM() to retrieve snps from locations
biomaRt getBM R
updated 15 days ago by 43k • written 5.2 years ago by ▴ 600
7
votes
10
replies
2.7k
views
6 follow
Batch effect correction to compare differentially expressed genes across datasets
batch batch-effect DESeq2 rna-seq
updated 15 days ago by 43k • written 2.0 years ago by ▴ 60
7
votes
20
replies
6.4k
views
7 follow
Repeat masked gtf files from ensembl
ensembl RNA-Seq genome
updated 21 days ago by ▴ 200 • written 4.3 years ago by ▴ 80
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma microarray DEA batch-effect
updated 14 days ago by 43k • written 4.7 years ago by ▴ 60
6
votes
0
replies
201
views
Herald: The Biostar Herald for Monday, April 15, 2024
herald
17 days ago by Biostar 2.7k
6
votes
8
replies
2.1k
views
Simple explanation and usage of WGCNA package?
wgcna RNA-Seq ChIP-Seq
updated 24 days ago by • 0 • written 3.9 years ago by ▴ 120
6
votes
6
replies
4.4k
views
10x to cloupe
single-cell-transcriptomics 10x
23 days ago by firestar ★ 1.6k
6
votes
17
replies
6.6k
views
Can you add a label key to heatscatter plot in R?
heatscatter visualization R
updated 15 days ago by 43k • written 9.6 years ago by ▴ 100
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat RNA-Seq Limma DESeq2 batch-effect
updated 13 days ago by 43k • written 5.0 years ago by ▴ 140
6
votes
11
replies
3.3k
views
Collapsing probesets to genes on WGCNA
WGCNA gene-expression R
updated 15 days ago by 43k • written 5.3 years ago by ▴ 120
6
votes
8
replies
590
views
BRAKER3 genome annotation
annotation BRAKER3 genome
updated 15 days ago by 14k • written 17 days ago by ▴ 40
6
votes
10
replies
1.9k
views
A guide to modern genome assembly
long-reads illumina genome-assembly
updated 27 days ago by 43k • written 2.6 years ago by ★ 1.9k
6
votes
4
replies
1.5k
views
RNA-Seq: X samples and X batches
RNA-Seq edgeR DESeq2 Batch-Effect
updated 15 days ago by 43k • written 5.2 years ago by ▴ 40
6
votes
4
replies
2.2k
views
Is there a way to get RNAFold output for multifasta in tabular format?
RNAFold
updated 15 days ago by • 0 • written 4.6 years ago by ▴ 40
6
votes
2
replies
1.5k
views
Writing a batch script for analyzing RNA-Seq data
RNA-Seq quantification alignment
updated 15 days ago by 43k • written 5.2 years ago by ▴ 250
6
votes
0
replies
2.6k
views
Tool: Immuno-Navigator, a batch-corrected database for gene coexpression in the immune system
gene-co-expression batch-effect immunology
updated 13 days ago by 43k • written 7.0 years ago by ▴ 80
6
votes
10
replies
2.3k
views
Why different DEGs between my result and the author's result?
limma microarray differential-gene-expression
updated 23 days ago by 43k • written 6.1 years ago by ▴ 170
6
votes
3
replies
198
views
Interpretting IGV output
IGV
updated 10 days ago by 8.7k • written 10 days ago by ▴ 30
6
votes
3
replies
1.1k
views
How to normalize long-read RNA-seq data for comparison with short-reads
RNAseq long-reads normalization short-reads
updated 29 days ago by 13k • written 15 months ago by ▴ 30
5
votes
3
replies
333
views
Best genome browser for manual curation of gene structure(s)?
structure gene
updated 20 days ago by ★ 3.8k • written 21 days ago by ★ 5.3k
5
votes
5
replies
149
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA DADA2 metabarcoding
updated 2 hours ago by ▴ 30 • written 6 hours ago by ▴ 150
5
votes
5
replies
872
views
Blacklist for bacterial genome [ChIPseq]?
ChIPseq Blacklist
updated 19 days ago by 43k • written 10 months ago by ▴ 30
5
votes
4
replies
673
views
How to compare the quality of assemblies
nextdenovo assembly hifiasm pacbio
8 days ago by kirillkirilenko ▴ 40
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq bulk-RNASeq RNA-Seq single-cell
updated 21 days ago by • 0 • written 3.8 years ago by ★ 1.8k
1,066 results • Page 2 of 22
Recent Votes
Comment: Bacterial plasmid analysis
Answer: Problem with data downloaded from Short Reads Archive (SRA)
Answer: Super ehancers
Comment: Bacterial plasmid analysis
Answer: Why employ normalization methods, and how can they be utilized in DEG analysis?
Answer: Why employ normalization methods, and how can they be utilized in DEG analysis?
Answer: What analysis suitable to identify similarly expressed genes between two samples
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Recent Replies
Answer: Loss of 'var' using concatenation of AnnData objects by Hugo • 0
Similar question has been asked and answered on [scverse discourse](https://discourse.scverse.org/t/loosing-anndata-var-layer-when-using-sc…
Comment: Bacterial plasmid analysis by Zamin Iqbal ▴ 20
Hi Nicole. 1. The clustering will be quite different between pling and the rep types (because plasmids with one rep type can still be ve…
Comment: Do I need to go back and filter my long-reads? by Ram 43k
Do not delete posts that have received feedback. Engage with the user providing you feedback.
Answer: Download eQTL data of one specific gene for all tissues from GTEx by bk11 ★ 2.4k
Please kindly check your result here. You can click `csv` and download the date in this [link][1]. **OR** If you prefer to use R, there i…
Comment: RNAseq one control two conditions, shared and exclusive genes by matteo.levorato • 0
but why not a single matrix with the 3 different condition and then by lfcShrink function get the DEGs of each condition?
Answer: Super ehancers by jared.andrews07 ★ 16k
Sure, you can run it on them. Stitching tends to happen less frequently since the ATAC peaks are generally less wide than H3K27ac, but it'l…
Answer: What purposes can TPM values be used for? by jared.andrews07 ★ 16k
TPMs cannot be used for intersample comparisons, but they can be used for intrasample comparisons (e.g. comparing relative expression level…
Comment: Bacterial plasmid analysis by nicole.kavanagh • 0
Thank you so much for the recommendation and the very clear explanation , it's much appreciated. I have already made core-gene phylogenies/…
Comment: What purposes can TPM values be used for? by Adam ▴ 30
Have you run FASTQC and checked the mapping efficiency of WT3? > would running DESeq using TPM values help solve my problem? No, DESeq sh…
Answer: How goes gene length effect the number of reads mapped by i.sudbery 19k
See my answer about the what hows and whens of RNA-seq normalisation here: https://www.biostars.org/p/9586553/#9586566
Comment: What purposes can TPM values be used for? by dsull ★ 5.9k
Since you have mutant vs wild-type, using DESeq2 is the right thing to do. Rather than showing a small table of numbers, you should make a …
Answer: What purposes can TPM values be used for? by i.sudbery 19k
See my post here for more details on RNA-seq normalisation: https://www.biostars.org/p/9586553/#9586566 In short, TPM normalises for ge…
Comment: Bacterial plasmid analysis by Zamin Iqbal ▴ 20
I vote for this, it's the best! (but also, I am Daria's PhD supervisor so I am biased). Preprint out soon(ish) [no pressure Daria!]
Comment: Downsampling long-read BAM files by GenoMax 142k
Is this what you used ultimately? Did this tool satisfy the "specific average depth" requirement? You could accept (green check mark) this…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory by Estevão • 0
Thank you. My budget is around 20 thousand dollars.
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