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887 results • Page 1 of 18
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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
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
29
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split fastq
updated 11 days ago by • 0 • written 12.8 years ago by ★ 1.7k
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
38
votes
24
replies
2.1k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq STAR NGS Illumina
updated 13 days ago by 19k • written 16 days ago by ▴ 580
9
votes
23
replies
9.8k
views
Tool: BioLabDonkey - new Mac program for molecular biologists
software biolabdonkey
2 days ago by vytarasov ▴ 180
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 26 days ago by 43k • written 5.4 years ago by ▴ 130
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
22
votes
18
replies
6.2k
views
about batch correction in scRNA-seq
scRNA scRNA-seq batch-effect
updated 25 days ago by 43k • written 4.6 years ago by ★ 1.4k
6
votes
17
replies
6.6k
views
Can you add a label key to heatscatter plot in R?
heatscatter visualization R
updated 27 days ago by 43k • written 9.6 years ago by ▴ 100
8
votes
16
replies
1.1k
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 17 days ago by ★ 2.4k • written 9 weeks ago by • 0
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
7
votes
16
replies
880
views
How many reads for WGS Sequencing?
WGS Bacterial-Genomics
15 days ago by Ruqaiya • 0
34
votes
16
replies
20k
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
4
votes
15
replies
1.7k
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 10 days ago by ★ 7.1k • written 5 months ago by ▴ 10
13
votes
14
replies
873
views
High Malat-1 expression in single cell data
single-cell
updated 6 days ago by ▴ 40 • written 14 days ago by ▴ 40
1
vote
14
replies
2.4k
views
Extract gRNA sequence using cutadapt
cutadapt trimming crispr sequencing
updated 11 days ago by 142k • written 4.5 years ago by ▴ 20
10
votes
14
replies
698
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 6 days ago by 142k • written 12 days ago by • 0
4
votes
13
replies
995
views
RNAseq of primary tumor and metastases in two different organ
metastases RNA-seq DEG R
updated 27 days ago by ★ 1.7k • written 4 weeks ago by • 0
0
votes
13
replies
3.6k
views
6 follow
Tax4Fun2 - error
tax4fun silva blast
updated 19 days ago by • 0 • written 2.2 years ago by ▴ 10
2
votes
13
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 1 day ago by • 0 • written 4.8 years ago by ▴ 60
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation reference panel
updated 3 days ago by ▴ 50 • written 6.4 years ago by ▴ 490
5
votes
13
replies
1.8k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 23 days ago by 82k • written 24 days ago by ★ 1.7k
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 25 days ago by • 0 • written 12.1 years ago by ★ 2.9k
4
votes
12
replies
4.9k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation Experience Illumina Mouse
updated 4 days ago by ▴ 180 • written 3.0 years ago by ▴ 20
8
votes
12
replies
1.9k
views
Metric to use for RNAseq expression matrix
gene-expression TPM RNA-Seq counts batch-effect
26 days ago by Ram 43k
30
votes
12
replies
3.9k
views
Trying to understand the maths behind one Limma function
limma RNA-Seq batch-effect
updated 28 days ago by 43k • written 4.0 years ago by ▴ 330
11
votes
12
replies
1.1k
views
Downloaded pdb's on rcsb.org
rcsb pdb
updated 25 days ago by 43k • written 25 days ago by • 0
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
9
votes
12
replies
4.2k
views
Batch effect, how to create a model matrix
RNA-Seq deseq2 batch-effect
updated 26 days ago by 43k • written 5.0 years ago by ▴ 330
25
votes
11
replies
3.8k
views
6 follow
Forum: Site Use Guidelines
meta biostars Guidelines
updated 20 days ago by 43k • written 14.6 years ago by 100k
4
votes
11
replies
866
views
Redirection of Duplicate PMIDs
pubmed pmid
updated 20 days ago by 4.2k • written 21 days ago by • 0
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 17 days ago by ★ 3.8k • written 10.8 years ago by ▴ 920
2
votes
11
replies
977
views
Questions about a bug when transferring cram file to bam file
sequence samtools bcftools
updated 14 days ago by ★ 1.2k • written 26 days ago by • 0
0
votes
11
replies
695
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
18 days ago by atowns21 • 0
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 27 days ago by 43k • written 5.0 years ago by 47k
0
votes
11
replies
483
views
In IGV is this a heterogeneous mutation or false call?
mutations IGV heterogeneous
1 day ago by Tuck898 • 0
6
votes
11
replies
3.4k
views
Collapsing probesets to genes on WGCNA
WGCNA gene-expression R
updated 27 days ago by 43k • written 5.3 years ago by ▴ 120
1
vote
11
replies
5.5k
views
Truncated Bam Error
R next-gen sequencing software error
updated 8 days ago by • 0 • written 6.1 years ago by ▴ 20
3
votes
11
replies
6.0k
views
Modifying R pairs() function
plotMEpairs WGCNA R
updated 27 days ago by 43k • written 6.5 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
0
votes
10
replies
593
views
Low mapping rate with Salmon
RNA-seq Salmon Quantification
updated 13 days ago by 19k • written 21 days ago by • 0
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 25 days ago by 43k • written 4.6 years ago by ▴ 140
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 27 days ago by 43k • written 7.5 years ago by • 0
1
vote
10
replies
1.0k
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq DESeq2 DNA-contamination
19 days ago by DKA ▴ 40
8
votes
10
replies
806
views
bash script
whole-genome-sequencing
updated 28 days ago by 43k • written 5 weeks ago by ▴ 30
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 27 days ago by 43k • written 2.1 years ago by ▴ 60
1
vote
10
replies
4.0k
views
Error in CIBERSORTx
RNA-seq CIBERSORT LM22
updated 29 days ago by ▴ 330 • written 19 months ago by • 0
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma microarray DEA batch-effect
updated 26 days ago by 43k • written 4.7 years ago by ▴ 60
40
votes
10
replies
42k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma sva Combat batch-effect
updated 14 days ago by ▴ 40 • written 6.8 years ago by ★ 1.3k
887 results • Page 1 of 18
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Answer: Is there any way to modify this pie chart ?
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
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Comment: What does the 'E%' represent in BUSCO results?
Answer: What does the 'E%' represent in BUSCO results?
Answer: Combine Two Affymetrix Datasets With Same Platform
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Recent Replies
Comment: Is it necessary to do genotype quality filteration after snp calling with GATK by IdaHao0921 • 0
The species I study is not a model species, VQSR can not be applied here. I already used gatk hard-filtering. I mean, after hard-filtering,…
Answer: Overlapping Ranges within Granges object by Alex Reynolds 35k
If you're not tied to Granges, you could use `bedmap --fraction-both 0.1` to require at least 10% overlap between reference and map regions…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred by Vijith ▴ 30
By doing some online search, I tried installing one module `cpan Bio::DB::Fasta` and it is running like a never-ending installation process…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred by Vijith ▴ 30
I have tried installing AGAT. But it failed the tests. …
Comment: BWA alignment by ATpoint 82k
That is not what the logs above tell, but good you solved it.
Answer: Inquiry about deseq2 transformation by ATpoint 82k
The transformations first correct for sequencing depth (and [composition][1]) and then apply the variance stabilization / regularization. N…
Answer: The total expressed genes in RNA-Seq data by ATpoint 82k
There is no robust definition of "expressed" genes, this has been asked many times before. edgeR doesn't care about "expressed", it cares (…
Answer: What is the bin size for Bamcompare? by ATpoint 82k
It is the number of adjacent bases that are aggregated (binned) into a single value. I find binning not optimal, and would always set this …
Comment: Is it necessary to do genotype quality filteration after snp calling with GATK by Pierre Lindenbaum 161k
see VQSR https://gatk.broadinstitute.org/hc/en-us/articles/360035531612-Variant-Quality-Score-Recalibration-VQSR and https://gatk.broadinst…
Comment: Snakemake wrapper issue by Matvii Mykhailichenko • 0
Hi, I kind of did and kind of didn't: I stopped trying to use snakemake( I remember that it's a lot of hustle to install pickard, maybe you…
Answer: Is there any way to modify this pie chart ? by marco.barr ▴ 110
Hi, you can add the labels outside chart using `geom_label_repel` from `ggrepel` package. Check out this guide [https://r-charts.com/part…
Answer: Snakemake wrapper issue by Wei-Chen Pan • 0
Hi, did you solve your problem ? I also encounter same issue but it's `wrapper:"v3.9.0/bio/picard/mergevcfs"`. In my log file, it said:…
Comment: What does the 'E%' represent in BUSCO results? by Philipp Bayer 8.5k
No worries! I found the commit with the maths too: https://gitlab.com/ezlab/busco/-/blame/master/src/busco/busco_tools/hmmer.py?page=2#L135…
Comment: What does the 'E%' represent in BUSCO results? by 林明德 • 0
Thank you for your answer! It really helped me resolve a doubt!
Answer: What does the 'E%' represent in BUSCO results? by Philipp Bayer 8.5k
Ah your edit solved this. 50 BUSCOs contain internal stop codons, indicating they might be erroneous gene models, or the genes themselves a…
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