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928 results • Page 1 of 19
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87
votes
24
replies
23k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 22 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
15 days ago by Kevin Blighe 87k
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 21 days ago by • 0 • written 12.1 years ago by ★ 2.9k
40
votes
10
replies
42k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma sva Combat batch-effect
updated 10 days ago by ▴ 40 • written 6.8 years ago by ★ 1.3k
38
votes
24
replies
2.0k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq STAR NGS Illumina
updated 10 days ago by 19k • written 12 days ago by ▴ 580
34
votes
16
replies
20k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read length bam
updated 21 days ago by ▴ 10 • written 10.2 years ago by ▴ 180
30
votes
12
replies
3.9k
views
Trying to understand the maths behind one Limma function
limma RNA-Seq batch-effect
updated 24 days ago by 43k • written 4.0 years ago by ▴ 330
29
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split fastq
updated 7 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 16 days ago by 43k • written 14.6 years ago by 100k
23
votes
11
replies
4.9k
views
7 follow
Code golf: detecting homopolymers of length N in the (human) genome
code golf fasta homopolymer repeat
updated 23 days ago by 43k • written 5.0 years ago by 47k
23
votes
23
replies
9.9k
views
6 follow
How to see if adjusting batch effect in RNA-seq is working or not
RNA-Seq removeBatchEffect batch-effect edger
updated 22 days ago by 43k • written 5.3 years ago by ▴ 130
22
votes
18
replies
6.2k
views
about batch correction in scRNA-seq
scRNA scRNA-seq batch-effect
updated 21 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 14 days ago by ★ 3.8k • written 10.8 years ago by ▴ 920
16
votes
12
replies
7.4k
views
10 follow
how to split multi-fasta file into single fasta file named by header
genome perl python3 bash python
updated 7 days ago by ▴ 10 • written 3.1 years ago by ▴ 120
15
votes
6
replies
1.3k
views
6 follow
VCF to human friendly form?
vcf visualization
updated 25 days ago by 161k • written 20 months ago by ▴ 10
14
votes
2
replies
7.0k
views
Trouble with Pilon installation
polishing pilon installation
updated 15 days ago by • 0 • written 7.3 years ago by ★ 1.4k
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva combat batch-effect
updated 23 days ago by 43k • written 6.8 years ago by ★ 1.3k
13
votes
14
replies
818
views
High Malat-1 expression in single cell data
single-cell
updated 2 days ago by ▴ 40 • written 11 days ago by ▴ 40
11
votes
9
replies
7.0k
views
How to choose method to integrate different patient sample together in Seurat
Seurat scRNA batch-effect harmony
updated 22 days ago by 43k • written 4.2 years ago by ▴ 80
11
votes
12
replies
1.1k
views
Downloaded pdb's on rcsb.org
rcsb pdb
updated 21 days ago by 43k • written 21 days ago by • 0
11
votes
9
replies
11k
views
10 follow
Genome assembly statistical tools
Assembly statistics
updated 27 days ago by • 0 • written 4.8 years ago by ▴ 10
10
votes
6
replies
14k
views
7 follow
How To Identify The 16S Rrna Gene Sequence In A Genome
updated 22 days ago by 6.4k • written 10.9 years ago by ▴ 10
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 3 days ago by 161k • written 5.7 years ago by ▴ 180
10
votes
14
replies
665
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 3 days ago by 142k • written 8 days ago by • 0
10
votes
36
replies
5.9k
views
Design in DESeq: Can you combine explicit and implicit batch effect correction in (SVA+Metadata Variables)?
SVA batch-effect DESeq2 R
updated 23 days ago by 43k • written 5.7 years ago by ▴ 620
10
votes
6
replies
10.0k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly rna-seq alignment
updated 14 days ago by ★ 5.1k • written 6.0 years ago by ▴ 510
10
votes
7
replies
7.1k
views
6 follow
Convert GVF to VCF
vcf
updated 24 days ago by • 0 • written 9.3 years ago by ▴ 970
10
votes
3
replies
293
views
TFs and Gene databases
Transcription-factor Target Regulatory-Networks
updated 2 days ago by ▴ 180 • written 2 days ago by • 0
9
votes
10
replies
4.4k
views
Using rnaseq reference sample across batches
RNA-Seq batch-effect
updated 23 days ago by 43k • written 7.4 years ago by ▴ 30
9
votes
12
replies
4.1k
views
Batch effect, how to create a model matrix
RNA-Seq deseq2 batch-effect
updated 22 days ago by 43k • written 5.0 years ago by ▴ 330
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 21 days ago by 43k • written 4.6 years ago by ▴ 140
9
votes
4
replies
2.0k
views
Integration of RNA-Seq data with microarray data
microarray RNA-Seq batch-effect R
updated 23 days ago by 43k • written 4.0 years ago by ▴ 30
9
votes
3
replies
7.0k
views
EdgeR-GLMs correcting for batch effects
RNA-Seq edgeR Batch-Effect
updated 21 days ago by 43k • written 10.0 years ago by ▴ 250
8
votes
12
replies
1.9k
views
Metric to use for RNAseq expression matrix
gene-expression TPM RNA-Seq counts batch-effect
22 days ago by Ram 43k
8
votes
6
replies
2.6k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 22 days ago by 3.0k • written 2.0 years ago by ▴ 230
8
votes
5
replies
6.3k
views
ISCN annotation for SV/CN VCF files
SV
written 8 months ago by ▴ 60
8
votes
8
replies
718
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 15 days ago by 14k • written 16 days ago by ▴ 10
8
votes
10
replies
792
views
bash script
whole-genome-sequencing
updated 24 days ago by 43k • written 4 weeks ago by ▴ 30
8
votes
5
replies
1.3k
views
Classifying repeat features from Ensembl
ensembl repeat
updated 25 days ago by ▴ 210 • written 16 months ago by ★ 1.4k
8
votes
16
replies
1.1k
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 13 days ago by ★ 2.4k • written 9 weeks ago by • 0
7
votes
2
replies
3.7k
views
Timeout on getBM() to retrieve snps from locations
biomaRt getBM R
updated 23 days ago by 43k • written 5.2 years ago by ▴ 600
7
votes
16
replies
781
views
How many reads for WGS Sequencing?
WGS Bacterial-Genomics
11 days ago by Ruqaiya • 0
7
votes
7
replies
1.7k
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 24 days ago by ★ 2.5k • written 25 days ago by • 0
7
votes
10
replies
2.8k
views
6 follow
Batch effect correction to compare differentially expressed genes across datasets
batch batch-effect DESeq2 rna-seq
updated 23 days ago by 43k • written 2.1 years ago by ▴ 60
7
votes
2
replies
309
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 16 days ago by ▴ 400 • written 17 days ago by • 0
7
votes
3
replies
1.2k
views
biomaRt::getSequence - Invalid type argument
biomaRt R
updated 23 days ago by 43k • written 3.9 years ago by ▴ 700
7
votes
6
replies
558
views
Filtering sam or bam file with maximum matching region
crisper-edited alignment match
18 days ago by analyst ▴ 50
7
votes
1
reply
154
views
Tutorial: removeBatchEffect explained using base R linear models
limma effects batch removebatcheffects
updated 3 days ago by 14k • written 3 days ago by ▴ 360
7
votes
3
replies
4.6k
views
how to deal with batch effect in TCGA RNA-seq dataset
TCGA RNA-Seq batch-effect
updated 22 days ago by 43k • written 5.1 years ago by ▴ 100
7
votes
3
replies
2.9k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
updated 21 days ago by 6.4k • written 16 months ago by ▴ 130
928 results • Page 1 of 19
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Comment: Question about methylation location
Comment: Question about methylation location
Comment: Question about methylation location
How to use minimap2?
Comment: RNA seq analysis
Comment: Filtering Multi-sample VCF file for all except one Genotype
Truncated metadata file report from ENA Portal API
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Comment: cellranger error message by Max • 0
I think the problem is your fastq_id. This should also read "RabhiN_PHLGEX". Hope this helps!
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK by Giulio Genovese ▴ 390
@yokofakun is correct. Also, do notice that the GATK option `--RECOVER_SWAPPED_REF_ALT True` does not work with indels. In general, if your…
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK by Pierre Lindenbaum 161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK by Pierre Lindenbaum 161k
I think this is useless, in the gatk doc: > For each variant, the tool will look for the target coordinate, reverse-complement and left-al…
Comment: Too many unpaired forward reads found by Trimmomatic by GenoMax 142k
Ideally you will know which adapters to use but if you don't then programs like `fastp` can auto-detect them. You could also use `bbduk.sh`…
Comment: UMI-Tools knee-method has great influence on the results of white list by i.sudbery 19k
With the `--read2-only` option (which isn't available yet on the bioconda version), this will complain about a lack of `--bc-pattern`. How…
Comment: samtools tview symbols by Ruqaiya • 0
What does the star mean then ?
Comment: RNA seq analysis by prifa ▴ 10
it's raw data **fastq.gz**, so for example I have 4 different samples from different tissue, sample A with 3 replicates, samples B,C and D …
Answer: Filtering Multi-sample VCF file for all except one Genotype by Pierre Lindenbaum 161k
> The goal is to remove all the variants which are unique to the KWSBambina sample. using jvarkit vcffilterjdk https://jvarkit.readthedo…
Comment: Too many unpaired forward reads found by Trimmomatic by SilhouetteQ • 0
The first example used the adapter file NexteraPE-PE.fa, but it generated more than 50% unpaired data...... The content of NexteraPE-PE.fa…
Comment: Filtering Multi-sample VCF file for all except one Genotype by schmince • 0
Ok so I definitely didn't understand at first what my goal was. The goal is to remove all the variants which are unique to the KWSBambina…
Comment: Question about methylation location by dthorbur ★ 1.9k
What data do you have? Generally, you start with sequencing data, which you need to clean and then map to a reference genome. Then dependin…
Comment: Too many unpaired forward reads found by Trimmomatic by GenoMax 142k
> when I didn't provide the adapter file Still see the file here `ILLUMINACLIP:./NexteraPE-PE.fa:2:30:10 `, unless that is an empty file.
Comment: Too many unpaired forward reads found by Trimmomatic by SilhouetteQ • 0
Interestingly, when I didn't provide the adapter file, the number of unpaired forward reads was significantly reduced: TrimmomaticPE…
Comment: Alignment of samples with spike-in by GenoMax 142k
> but then if you only allow to map uniquely mapped reads, you are losing spike-in information, How so? Spike-in's are generally unique s…
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