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1,106 results • Page 2 of 23
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8
votes
12
replies
3.5k
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Why should ATAC-seq mapped reads be shifted +4 and -5 for +strand and -strand, respectively
ATAC-seq
updated 27 days ago by • 0 • written 3.4 years ago by ▴ 40
8
votes
2
replies
788
views
News: FINAL CALL - Single-Cell RNA-Seq Data Analysis: A Practical Introduction (May 6-8, 2024 in Berlin)
single-cell sequencing
25 days ago by David Langenberger 11k
8
votes
6
replies
2.6k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 12 days ago by 3.0k • written 24 months ago by ▴ 230
8
votes
16
replies
910
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 3 days ago by ★ 2.4k • written 7 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
12 days ago by Ram 43k
8
votes
10
replies
726
views
bash script
whole-genome-sequencing
updated 14 days ago by 43k • written 22 days ago by ▴ 30
8
votes
6
replies
2.5k
views
Batch effect removal with the help of sva
SVA batch-effect gene-expression
updated 21 days ago by 43k • written 3.5 years ago by ▴ 240
8
votes
5
replies
1.2k
views
Classifying repeat features from Ensembl
ensembl repeat
updated 15 days ago by ▴ 200 • written 16 months ago by ★ 1.4k
8
votes
8
replies
608
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 5 days ago by 14k • written 6 days ago by ▴ 10
8
votes
5
replies
5.5k
views
ISCN annotation for SV/CN VCF files
SV
written 8 months ago by ▴ 60
8
votes
4
replies
3.0k
views
Read count correlation between samples
differential-gene-expression RNA-seq
updated 20 days ago by 43k • written 6.5 years ago by ★ 1.6k
8
votes
3
replies
371
views
How to extract rows with specific values in R for all the columns?
R
26 days ago by Lakshmi ▴ 20
8
votes
6
replies
633
views
The bioinformatics paper reappears, but the results are significantly different from the original results
reproducibility
25 days ago by jiao ▴ 40
7
votes
8
replies
682
views
6 follow
How to BLAST more than 5 sequences against UniProt database?
BLAST Protein UniProt
25 days ago by Riq ▴ 50
7
votes
20
replies
6.4k
views
7 follow
Repeat masked gtf files from ensembl
ensembl RNA-Seq genome
updated 18 days ago by ▴ 200 • written 4.3 years ago by ▴ 80
7
votes
4
replies
1.9k
views
AlphaFold 2 alternatives
protein-structure alphafold
updated 27 days ago by 43k • written 17 months ago by ★ 2.5k
7
votes
3
replies
1.2k
views
biomaRt::getSequence - Invalid type argument
biomaRt R
updated 13 days ago by 43k • written 3.9 years ago by ▴ 680
7
votes
2
replies
275
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 6 days ago by ▴ 390 • written 7 days ago by • 0
7
votes
7
replies
1.4k
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 14 days ago by ★ 2.5k • written 15 days ago by • 0
7
votes
4
replies
2.1k
views
filtering genes by pearson correlation
correlation RNA-Seq R
updated 13 days ago by 43k • written 6.1 years ago by ▴ 120
7
votes
3
replies
2.8k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
updated 11 days ago by 6.4k • written 16 months ago by ▴ 130
7
votes
3
replies
4.6k
views
how to deal with batch effect in TCGA RNA-seq dataset
TCGA RNA-Seq batch-effect
updated 12 days ago by 43k • written 5.1 years ago by ▴ 100
7
votes
7
replies
573
views
Can you suggest a protein PDB that has two chainst but only 50 total number of atoms?
protein pdb protein-databank
updated 17 days ago by 4.6k • written 17 days ago by • 0
7
votes
2
replies
3.7k
views
Timeout on getBM() to retrieve snps from locations
biomaRt getBM R
updated 13 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 13 days ago by 43k • written 2.0 years ago by ▴ 60
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 13 days ago by 43k • written 21 months ago by ▴ 20
7
votes
6
replies
511
views
Filtering sam or bam file with maximum matching region
crisper-edited alignment match
8 days ago by analyst ▴ 30
7
votes
6
replies
1.3k
views
using different microarray datasets (meta-analysis?) for DEG pipeline
microarray meta-analysis DEG batch-effect
updated 12 days ago by 43k • written 4.9 years ago by ▴ 30
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq SNP
updated 4 days ago by ▴ 850 • written 6.1 years ago by ▴ 10
7
votes
8
replies
670
views
Why are the basics so complicated? Basic coverage filtering for VCF files
filter vcf coverage
updated 17 days ago by ▴ 40 • written 21 days ago by ▴ 40
7
votes
7
replies
1.0k
views
Prediction tools summary - zero values
statistics
updated 13 days ago by • 0 • written 6 months ago by ▴ 50
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma microarray DEA batch-effect
updated 12 days ago by 43k • written 4.7 years ago by ▴ 60
6
votes
4
replies
2.2k
views
Is there a way to get RNAFold output for multifasta in tabular format?
RNAFold
updated 12 days ago by • 0 • written 4.6 years ago by ▴ 40
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat RNA-Seq Limma DESeq2 batch-effect
updated 11 days ago by 43k • written 5.0 years ago by ▴ 140
6
votes
8
replies
576
views
BRAKER3 genome annotation
annotation BRAKER3 genome
updated 13 days ago by 14k • written 15 days ago by ▴ 40
6
votes
17
replies
6.6k
views
Can you add a label key to heatscatter plot in R?
heatscatter visualization R
updated 13 days ago by 43k • written 9.6 years ago by ▴ 100
6
votes
2
replies
1.5k
views
Writing a batch script for analyzing RNA-Seq data
RNA-Seq quantification alignment
updated 13 days ago by 43k • written 5.2 years ago by ▴ 250
6
votes
3
replies
191
views
Interpretting IGV output
IGV
updated 8 days ago by 8.7k • written 8 days ago by ▴ 30
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 11 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 20 days ago by 43k • written 6.1 years ago by ▴ 170
6
votes
0
replies
198
views
Herald: The Biostar Herald for Monday, April 15, 2024
herald
14 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 22 days ago by • 0 • written 3.9 years ago by ▴ 120
6
votes
4
replies
1.5k
views
RNA-Seq: X samples and X batches
RNA-Seq edgeR DESeq2 Batch-Effect
updated 13 days ago by 43k • written 5.2 years ago by ▴ 40
6
votes
11
replies
3.3k
views
Collapsing probesets to genes on WGCNA
WGCNA gene-expression R
updated 13 days ago by 43k • written 5.2 years ago by ▴ 120
6
votes
6
replies
4.4k
views
10x to cloupe
single-cell-transcriptomics 10x
21 days ago by firestar ★ 1.6k
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 27 days ago by 13k • written 15 months ago by ▴ 30
6
votes
10
replies
1.9k
views
A guide to modern genome assembly
long-reads illumina genome-assembly
updated 24 days ago by 43k • written 2.6 years ago by ★ 1.9k
5
votes
2
replies
1.8k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq batch batch-effect sequencing
updated 13 days ago by 43k • written 3.0 years ago by ▴ 60
5
votes
4
replies
335
views
I'm new to cell ranger. Can single cells prepared with a protocol other than the 10x genomics protocol not be processed with cell ranger?
cellranger scRNA-seq 10x
14 days ago by Spring • 0
5
votes
13
replies
1.3k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 9 days ago by 82k • written 10 days ago by ★ 1.7k
1,106 results • Page 2 of 23
Recent Votes
Comment: MA plot of shrunken fold change
Answer: Single-stranded RNA-seq: strandedness of samples
Comment: NGS forensics: how to know if data is fabricated
Answer: blasting genome contigs against local SILVA 16S RNA database
blasting genome contigs against local SILVA 16S RNA database
Comment: Integrate transcriptomic data and proteomics data.
Comment: MA plot of shrunken fold change
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Recent Replies
Comment: unable to get feature count results by GenoMax 141k
Galaxy specific questions are best posted to their support site: https://help.galaxyproject.org/ That said, problems with counting are lik…
Comment: Landmark gene selection in L1000. by GenoMax 141k
Link for the data is included above.
Comment: Introduce SNPs on FASTA by GenoMax 141k
If you have specific changes you want to make then you can edit the fasta file accordingly.
Answer: Taking the difference of two VCFs (or removing singletons) by Andres ▴ 20
I know this is an old question but when searching for filtering out singletons(and doubletons too) i found this post in the first results. …
Comment: NGS forensics: how to know if data is fabricated by i.sudbery 19k
In which case, I'd definately look at the distribution of read lengths, post trimming, and see if there is a discontinuity in the distribut…
Comment: Low mapping rate with Salmon by i.sudbery 19k
I would note that even on a good, polyA selected, RNA-seq run, I would only expect 60-75% of mapped reads to map to protein coding exons.
Answer: FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last plac by David Langenberger 11k
:: FINAL CALL :: 8th Berlin Summer School in NGS Data Analysis 2024 - Only a few last places available
Comment: Low mapping rate with Salmon by Patadu94 • 0
Oh, then I will check the output file from featureCounts.
Comment: Low mapping rate with Salmon by Patadu94 • 0
How would I check if these reads are aligning to regions where there is no expressed sequence know? Should I follow the suggestion of i.sud…
Answer: Deseq2 by Jack Tierney ▴ 360
[This vignette][1] is a great place to start. [1]: https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.ht…
Comment: Genbank File Format by alenew.am • 0
Thanks, yes i have tried first here looking for a easier solution (for me), i didnt' know if this format was already available somewhere. t…
Comment: Genbank File Format by alenew.am • 0
Yes, it would be fine with an external solution, thanks for the reply
Answer: Polishing genome assembly by Michael 54k
If you have Hifi reads your error rate should already be quite good, therefore polishing with potentially longer and slightly more error-pr…
Comment: Integrate transcriptomic data and proteomics data. by Lluís R. ★ 1.2k
You don't need to subset for common features, there are tools that work for that like RGCCA, mixOmics. See for instance a classification [h…
Answer: Integrate transcriptomic data and proteomics data. by KABILAN ▴ 50
You can use R package named 'mixOmics' to integrate the datasets. Kindly go through the manual of this package.
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