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895 results • Page 1 of 18
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87
votes
24
replies
23k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 26 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
19 days ago by Kevin Blighe 88k
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 26 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 15 days ago by ▴ 40 • written 6.8 years ago by ★ 1.3k
38
votes
24
replies
2.2k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq STAR NGS Illumina
updated 14 days ago by 19k • written 17 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 25 days ago by ▴ 10 • written 10.3 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 29 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 12 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 21 days ago by 43k • written 14.6 years ago by 100k
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 27 days ago by 43k • written 5.4 years ago by ▴ 130
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 28 days ago by 43k • written 5.0 years ago by 47k
22
votes
18
replies
6.2k
views
about batch correction in scRNA-seq
scRNA scRNA-seq batch-effect
updated 26 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 18 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 11 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 29 days ago by 161k • written 20 months ago by ▴ 10
14
votes
2
replies
7.1k
views
Trouble with Pilon installation
polishing pilon installation
updated 19 days ago by • 0 • written 7.3 years ago by ★ 1.4k
13
votes
14
replies
882
views
High Malat-1 expression in single cell data
single-cell
updated 6 days ago by ▴ 40 • written 15 days ago by ▴ 40
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 27 days ago by 43k • written 6.8 years ago by ★ 1.3k
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 27 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 25 days ago by 43k • written 26 days ago by • 0
10
votes
6
replies
14k
views
7 follow
How To Identify The 16S Rrna Gene Sequence In A Genome
updated 26 days ago by 6.4k • written 10.9 years ago by ▴ 10
10
votes
7
replies
7.2k
views
6 follow
Convert GVF to VCF
vcf
updated 28 days ago by • 0 • written 9.3 years ago by ▴ 980
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 27 days ago by 43k • written 5.7 years ago by ▴ 620
10
votes
14
replies
718
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 7 days ago by 142k • written 13 days ago by • 0
10
votes
3
replies
314
views
TFs and Gene databases
Transcription-factor Target Regulatory-Networks
updated 6 days ago by ▴ 180 • written 7 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 18 days ago by ★ 5.1k • written 6.0 years ago by ▴ 520
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 7 days ago by 161k • written 5.8 years ago by ▴ 180
9
votes
12
replies
4.2k
views
Batch effect, how to create a model matrix
RNA-Seq deseq2 batch-effect
updated 27 days ago by 43k • written 5.0 years ago by ▴ 330
9
votes
3
replies
7.0k
views
EdgeR-GLMs correcting for batch effects
RNA-Seq edgeR Batch-Effect
updated 26 days ago by 43k • written 10.0 years ago by ▴ 250
9
votes
23
replies
9.8k
views
Tool: BioLabDonkey - new Mac program for molecular biologists
software biolabdonkey
3 days ago by vytarasov ▴ 180
9
votes
4
replies
2.0k
views
Integration of RNA-Seq data with microarray data
microarray RNA-Seq batch-effect R
updated 27 days ago by 43k • written 4.0 years ago by ▴ 30
9
votes
10
replies
4.5k
views
Using rnaseq reference sample across batches
RNA-Seq batch-effect
updated 27 days ago by 43k • written 7.4 years ago by ▴ 30
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 26 days ago by 43k • written 4.6 years ago by ▴ 140
9
votes
7
replies
7.1k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 3 days ago by • 0 • written 5.7 years ago by ▴ 20
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation reference panel
updated 4 days ago by ▴ 50 • written 6.4 years ago by ▴ 490
8
votes
16
replies
1.2k
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 18 days ago by ★ 2.4k • written 9 weeks ago by • 0
8
votes
8
replies
741
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 19 days ago by 14k • written 20 days ago by ▴ 10
8
votes
5
replies
6.4k
views
ISCN annotation for SV/CN VCF files
SV
written 8 months ago by ▴ 60
8
votes
5
replies
1.3k
views
Classifying repeat features from Ensembl
ensembl repeat
updated 29 days ago by ▴ 210 • written 16 months ago by ★ 1.4k
8
votes
6
replies
2.6k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 27 days ago by 3.0k • written 2.0 years ago by ▴ 230
8
votes
10
replies
807
views
bash script
whole-genome-sequencing
updated 29 days ago by 43k • written 5 weeks ago by ▴ 30
8
votes
12
replies
1.9k
views
Metric to use for RNAseq expression matrix
gene-expression TPM RNA-Seq counts batch-effect
27 days ago by Ram 43k
7
votes
3
replies
1.2k
views
biomaRt::getSequence - Invalid type argument
biomaRt R
updated 27 days ago by 43k • written 3.9 years ago by ▴ 700
7
votes
7
replies
1.8k
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 29 days ago by ★ 2.5k • written 29 days ago by • 0
7
votes
2
replies
3.7k
views
Timeout on getBM() to retrieve snps from locations
biomaRt getBM R
updated 27 days ago by 43k • written 5.3 years ago by ▴ 600
7
votes
16
replies
899
views
How many reads for WGS Sequencing?
WGS Bacterial-Genomics
15 days ago by Ruqaiya • 0
7
votes
3
replies
4.6k
views
how to deal with batch effect in TCGA RNA-seq dataset
TCGA RNA-Seq batch-effect
updated 27 days ago by 43k • written 5.1 years ago by ▴ 100
7
votes
6
replies
576
views
Filtering sam or bam file with maximum matching region
crisper-edited alignment match
23 days ago by analyst ▴ 50
7
votes
2
replies
319
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 20 days ago by ▴ 400 • written 22 days ago by • 0
7
votes
7
replies
1.1k
views
Prediction tools summary - zero values
statistics
updated 28 days ago by • 0 • written 7 months ago by ▴ 50
895 results • Page 1 of 18
Recent Votes
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file
A: Best de novo assembler for insect genome ?
Comment: sci-RNA-seq
The Biostar Herald for Monday, May 13, 2024
Answer: Finding variants within a subset of a BAM file
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
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Recent Replies
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr by Ram 43k
Please accept your own answer to mark the post as solved.
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file by Ram 43k
A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accep…
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file by Prawesh • 0
thanks, it's working now.
Comment: Genome Visualization Tools by GenoMax 142k
@cmdcolin has a great list here: https://github.com/cmdcolin/awesome-genome-visualization
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file by Trivas ★ 1.8k
You need to have indexed your bam/sam file using `samtools index`
Answer: Using ggplotly in R by jared.andrews07 ★ 16k
The simple answer is to plot it natively with plotly rather than use `ggplotly`. See [this stackoverflow answer](https://stackoverflow.com/…
Comment: Why does assigning genes with biomart give me different values than using a tran by GenoMax 142k
According to HUGO there is only one [**ZSCAN2 gene**][1] and it points to the first Ensembl gene ID (ENSG00000176371). Ensembl is annotatin…
Answer: RNAseq RNA content by noodle ▴ 580
There are many tools for this. I recommend [gatk (picard) CollectRnaSeqMetrics][1] or alternatively [RSeQC][2] and then run [multiqc][3…
Comment: Where to get the following bed file? by wyuan37 • 0
Hi, I emailed them and did get the bed file! Thank you so much.
Comment: Where to get the following bed file? by wyuan37 • 0
Thanks! Super helpful.
Answer: Post-imputation QC for input into GWAS analyses by LauferVA 4.2k
1. Imputation algorithms will output log files indicating, among other things, accuracy of imputation. We can't comment on specifics as we …
Comment: Using Cutadapt to trim adapters from paired-end small RNA sequence data by GenoMax 142k
You can simply ignore read 2. It is not adding any information since your small RNA's are going to be small and were completely sequenced b…
Comment: Overlapping Ranges within Granges object by ntsopoul ▴ 60
does this work with a single .bed file?
Comment: Finding variants within a subset of a BAM file by ramiro.barrantes • 0
Actually, I found a solution in downloading "bam slices" from TCGA ([https://docs.gdc.cancer.gov/API/Users_Guide/BAM_Slicing/][1]) , which …
Comment: Overlapping Ranges within Granges object by ntsopoul ▴ 60
![enter image description here][1]Here is some representative data and an image in igv of one gene. I have loaded the .bed file in igv. As …
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