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87
votes
24
replies
24k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 29 days ago by • 0 • written 3.6 years ago by 3.2k
76
votes
72
replies
20k
views
19 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
22 days ago by Kevin Blighe 88k
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 29 days ago by • 0 • written 12.1 years ago by ★ 2.9k
40
votes
10
replies
43k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma sva Combat batch-effect
updated 18 days ago by ▴ 40 • written 6.8 years ago by ★ 1.3k
38
votes
12
replies
31k
views
9 follow
How to systematically check if a bam file is truncated
Exomeseq
updated 5 hours ago by ▴ 170 • written 7.1 years ago by ▴ 240
38
votes
24
replies
2.2k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq STAR NGS Illumina
updated 17 days ago by 19k • written 20 days ago by ▴ 580
34
votes
16
replies
21k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read length bam
updated 28 days ago by ▴ 10 • written 10.3 years ago by ▴ 180
29
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split fastq
updated 15 days ago by • 0 • written 12.8 years ago by ★ 1.7k
25
votes
11
replies
3.8k
views
6 follow
Forum: Site Use Guidelines
meta biostars Guidelines
updated 24 days ago by 43k • written 14.6 years ago by 100k
22
votes
18
replies
6.2k
views
about batch correction in scRNA-seq
scRNA scRNA-seq batch-effect
updated 29 days ago by 43k • written 4.6 years ago by ★ 1.4k
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 21 days ago by ★ 3.8k • written 10.8 years ago by ▴ 920
16
votes
12
replies
7.5k
views
10 follow
how to split multi-fasta file into single fasta file named by header
genome perl python3 bash python
updated 14 days ago by ▴ 10 • written 3.2 years ago by ▴ 120
14
votes
2
replies
7.1k
views
Trouble with Pilon installation
polishing pilon installation
updated 23 days ago by • 0 • written 7.3 years ago by ★ 1.4k
13
votes
14
replies
911
views
High Malat-1 expression in single cell data
single-cell
updated 9 days ago by ▴ 40 • written 18 days ago by ▴ 40
11
votes
12
replies
1.2k
views
Downloaded pdb's on rcsb.org
rcsb pdb
updated 29 days ago by 43k • written 29 days ago by • 0
11
votes
3
replies
335
views
TFs and Gene databases
Transcription-factor Target Regulatory-Networks
updated 9 days ago by ▴ 200 • written 10 days ago by • 0
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 10 days ago by 161k • written 5.8 years ago by ▴ 180
10
votes
6
replies
14k
views
7 follow
How To Identify The 16S Rrna Gene Sequence In A Genome
updated 29 days ago by 6.4k • written 10.9 years ago by ▴ 10
10
votes
14
replies
774
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 10 days ago by 142k • written 16 days ago by • 0
10
votes
6
replies
10k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly rna-seq alignment
updated 21 days ago by ★ 5.1k • written 6.0 years ago by ▴ 520
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation reference panel
updated 7 days ago by ▴ 50 • written 6.4 years ago by ▴ 490
9
votes
10
replies
7.0k
views
Harmony batch correction vs. regressing out donor effect in Seurat
Seurat scRNA-seq Harmony RNA-seq batch-effect
updated 29 days ago by 43k • written 4.6 years ago by ▴ 140
9
votes
23
replies
9.8k
views
Tool: BioLabDonkey - new Mac program for molecular biologists
software biolabdonkey
6 days ago by vytarasov ▴ 180
9
votes
3
replies
7.0k
views
EdgeR-GLMs correcting for batch effects
RNA-Seq edgeR Batch-Effect
updated 29 days ago by 43k • written 10.0 years ago by ▴ 250
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 6 days ago by • 0 • written 5.7 years ago by ▴ 20
8
votes
8
replies
755
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 22 days ago by 14k • written 23 days ago by ▴ 10
8
votes
5
replies
6.5k
views
ISCN annotation for SV/CN VCF files
SV
written 8 months ago by ▴ 60
8
votes
16
replies
1.2k
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 21 days ago by ★ 2.5k • written 10 weeks ago by • 0
7
votes
16
replies
946
views
How many reads for WGS Sequencing?
WGS Bacterial-Genomics
18 days ago by Ruqaiya • 0
7
votes
1
reply
196
views
Tutorial: removeBatchEffect explained using base R linear models
limma effects batch removebatcheffects
updated 10 days ago by 14k • written 10 days ago by ▴ 360
7
votes
7
replies
6.0k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq SNP
updated 22 days ago by ▴ 860 • written 6.2 years ago by ▴ 10
7
votes
6
replies
595
views
Filtering sam or bam file with maximum matching region
crisper-edited alignment match
26 days ago by analyst ▴ 50
7
votes
2
replies
328
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 23 days ago by ▴ 400 • written 25 days ago by • 0
7
votes
3
replies
3.0k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
updated 28 days ago by 6.4k • written 16 months ago by ▴ 130
6
votes
7
replies
387
views
Longest transcript variant per gene
transcript longest variant orthofinder
5 days ago by sansan_96 ▴ 90
6
votes
3
replies
230
views
Interpretting IGV output
IGV
updated 25 days ago by 8.7k • written 25 days ago by ▴ 50
6
votes
4
replies
439
views
Forum: Ideal PC configurations and operating system for bioinformatics laboratory
PC
15 days ago by Estevão ▴ 10
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 29 days ago by 43k • written 7.1 years ago by ▴ 80
6
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing coverage
2 days ago by Arton ▴ 10
6
votes
4
replies
13k
views
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
trimmomatic paired-end
updated 6 days ago by • 0 • written 6.5 years ago by ▴ 130
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 5 days ago by • 0 • written 6.7 years ago by • 0
6
votes
2
replies
239
views
EdgeR - relationship between logFC and coefficients
differential-expression r edger
updated 7 days ago by ★ 7.2k • written 7 days ago by ▴ 10
6
votes
4
replies
266
views
Details on salmon index
Salmon
updated 8 hours ago by 6.6k • written 1 day ago by • 0
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat RNA-Seq Limma DESeq2 batch-effect
updated 29 days ago by 43k • written 5.0 years ago by ▴ 140
6
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon human bed v7 agilent all sureselect
updated 12 days ago by ▴ 10 • written 2.0 years ago by • 0
5
votes
2
replies
346
views
ChIP-seq datasets: input samples omitted?
ChIP-seq Normalization NGS
updated 18 days ago by 19k • written 21 days ago by ▴ 40
5
votes
5
replies
340
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA DADA2 metabarcoding
updated 15 days ago by ▴ 40 • written 15 days ago by ▴ 150
5
votes
4
replies
717
views
How to compare the quality of assemblies
nextdenovo assembly hifiasm pacbio
23 days ago by kirillkirilenko ▴ 40
5
votes
3
replies
758
views
Illumina reads preprocessing best practice for snp calling applications
Illumina snp
updated 28 days ago by • 0 • written 10 months ago by ▴ 310
5
votes
2
replies
437
views
Missing protein (VEGF-A) in String db
VGFA stringdb
updated 21 days ago by ▴ 10 • written 3 months ago by ▴ 20
760 results • Page 1 of 16
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Answer: How to download dbSNP153 vcf files in hg19/GRCH37 version
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Answer: TFs and Gene databases
A: Is there a software that can compare phylogenetic trees to each othe (face to fa
Comment: Differentially Expressed Genes between two conditions (scRNA, single GEO dataset
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Recent Replies
Answer: Design for complex RNA-Seq experiment using Deseq2 by swbarnes2 14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot by LauferVA 4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot by bk11 ★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool by ntsopoul ▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
Answer: Trimming tool by GenoMax 142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by bk11 ★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
Comment: Reconstruction of locus, order contigs by dthorbur ★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint I checked all transcripts of GAPDH. they all have 0 TPM.
Comment: how to treat the replicates while performing WGCNA by andres.firrincieli 3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
Comment: How to systematically check if a bam file is truncated by alanh ▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
Comment: How to handle duplicated genes in TCGA data? by Zhenyu Zhang ★ 1.2k
Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by Ram 43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
Comment: Reconstruction of locus, order contigs by BATMAN • 0
I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
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