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807 results • Page 2 of 17
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6
votes
4
replies
434
views
Forum: Ideal PC configurations and operating system for bioinformatics laboratory
PC
14 days ago by Estevão ▴ 10
6
votes
11
replies
3.4k
views
Collapsing probesets to genes on WGCNA
WGCNA gene-expression R
updated 29 days ago by 43k • written 5.3 years ago by ▴ 120
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 5 days ago by • 0 • written 6.5 years ago by ▴ 130
6
votes
3
replies
226
views
Interpretting IGV output
IGV
updated 24 days ago by 8.7k • written 24 days ago by ▴ 50
5
votes
7
replies
483
views
RNA seq analysis
DESeq RNA-seq
1 day ago by Jacek ▴ 20
5
votes
4
replies
717
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq EdgeR DEGs DESeq2
28 days ago by BioinfGuru ★ 1.7k
5
votes
5
replies
2.2k
views
batch effect in RNAseq analysis using tophat cufflinks pipeline
RNA-Seq tophat batch-effect cufflinks
updated 29 days ago by 43k • written 5.4 years ago by • 0
5
votes
3
replies
312
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 16 days ago by ★ 1.2k • written 16 days ago by • 0
5
votes
2
replies
2.6k
views
How do you evaluate the effectiveness of the batch effect algorithm?
Batch-Effect
updated 28 days ago by 43k • written 9.2 years ago by ▴ 110
5
votes
5
replies
324
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA DADA2 metabarcoding
updated 14 days ago by ▴ 30 • written 14 days ago by ▴ 150
5
votes
6
replies
594
views
Programmatically retrieving positions of protein active site residues
Uniprot PDB Proteins
updated 16 days ago by ▴ 760 • written 17 days ago by ▴ 40
5
votes
5
replies
661
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 13 days ago by • 0 • written 22 days ago by ★ 3.9k
5
votes
13
replies
2.0k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 26 days ago by 82k • written 27 days ago by ★ 1.7k
5
votes
4
replies
711
views
How to compare the quality of assemblies
nextdenovo assembly hifiasm pacbio
23 days ago by kirillkirilenko ▴ 40
5
votes
2
replies
345
views
ChIP-seq datasets: input samples omitted?
ChIP-seq Normalization NGS
updated 17 days ago by 19k • written 20 days ago by ▴ 40
5
votes
5
replies
307
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
9 days ago by Chris ▴ 280
5
votes
2
replies
436
views
Missing protein (VEGF-A) in String db
VGFA stringdb
updated 21 days ago by ▴ 10 • written 3 months ago by ▴ 20
5
votes
3
replies
758
views
Illumina reads preprocessing best practice for snp calling applications
Illumina snp
updated 27 days ago by • 0 • written 10 months ago by ▴ 310
4
votes
4
replies
2.9k
views
CNVkit for somatic copy number detection
cnv cnvkit exome WES
updated 2 days ago by • 0 • written 5.1 years ago by • 0
4
votes
2
replies
274
views
GRCh38.gmap file
gnomix gmap
12 days ago by lorena9132 ▴ 10
4
votes
2
replies
270
views
How can I analyze normalized expression data?
DEseq2 RNA-seq
8 days ago by mnx0723 • 0
4
votes
2
replies
1.9k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF SAM BAM GFF minimap2
updated 29 days ago by ▴ 130 • written 12 months ago by • 0
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 13 days ago by ★ 7.2k • written 5 months ago by ▴ 10
4
votes
4
replies
2.6k
views
Advice on Handling Batch Effect in ChIP-seq Experiment
ChIP-Seq batch-effect sequencing
updated 29 days ago by 43k • written 4.7 years ago by ▴ 20
4
votes
9
replies
2.7k
views
Tool: CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.3 years ago by • 0
4
votes
1
reply
198
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
2 days ago by J. ▴ 40
4
votes
3
replies
438
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc conda nextflow
updated 19 days ago by 3.2k • written 20 days ago by ▴ 40
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference 38build impute imputation
17 days ago by anna ▴ 20
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq RNA-Seq exon
updated 10 days ago by ▴ 30 • written 6.7 years ago by ★ 1.2k
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome sequencing singleton SNP filter
updated 16 days ago by ▴ 20 • written 9.7 years ago by ▴ 40
4
votes
9
replies
2.2k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing bowtie2 alignment samtools ngs
updated 13 days ago by • 0 • written 2.2 years ago by • 0
4
votes
5
replies
451
views
Figures are disappeared from html report of SnpEff
HTML SnpEff
17 days ago by analyst ▴ 50
4
votes
12
replies
4.9k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation Experience Illumina Mouse
updated 7 days ago by ▴ 180 • written 3.0 years ago by ▴ 20
4
votes
3
replies
2.9k
views
How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when run SamToFastq
samtofasq picard validatesamfile
updated 7 days ago by 161k • written 7 days ago by ★ 1.2k
4
votes
6
replies
801
views
7 follow
Heatmap and rna-seq
RNA-Seq Heatmap
updated 19 days ago by ★ 6.0k • written 23 days ago by ▴ 10
4
votes
7
replies
397
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
3 days ago by Chen • 0
4
votes
1
reply
254
views
LD-prune variants while maintaining a list of SNPs
snp vcf plink filtering independent
updated 10 days ago by 11k • written 12 days ago by ▴ 560
4
votes
2
replies
263
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 12 days ago by 43k • written 13 days ago by ▴ 40
4
votes
6
replies
4.0k
views
Correcting for batch effect in RNA-seq data
RNA-Seq batch-effect
updated 29 days ago by 43k • written 4.8 years ago by ▴ 30
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient molecule at bam DNA RG ends clipping damage
updated 8 days ago by ▴ 10 • written 2.5 years ago by • 0
4
votes
5
replies
3.4k
views
How to compare compare two Sam files to check mapping
alignment
updated 8 days ago by ▴ 90 • written 6.4 years ago by ▴ 60
4
votes
7
replies
604
views
To get p-values for the TPM
P-value TPM RSEM
updated 21 days ago by ★ 6.0k • written 22 days ago by • 0
4
votes
1
reply
353
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma voom R
17 days ago by pairedttest ▴ 10
4
votes
11
replies
880
views
Redirection of Duplicate PMIDs
pubmed pmid
updated 23 days ago by 4.2k • written 24 days ago by • 0
4
votes
7
replies
631
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
17 days ago by e.r.zakiev ▴ 210
4
votes
2
replies
3.8k
views
DESeq2 design and batch effect
RNA-Seq batch-effect DESeq2 Salmon
updated 28 days ago by 43k • written 6.6 years ago by ▴ 30
4
votes
8
replies
763
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs BED eqtl bedtools
updated 20 days ago by 35k • written 21 days ago by ▴ 10
4
votes
0
replies
157
views
Herald: The Biostar Herald for Monday, April 29, 2024
herald
17 days ago by Biostar 2.8k
4
votes
2
replies
373
views
Assume "yes" as the answer to any prompts with bioconda
docker container bioconda
updated 28 days ago by 8.6k • written 28 days ago by ▴ 20
4
votes
5
replies
4.3k
views
Tool: GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly Structural-Variation Variant-Calling
updated 6 hours ago by ▴ 520 • written 7.2 years ago by ★ 2.9k
807 results • Page 2 of 17
Recent Votes
Comment: switch off warning in blast command line
Forward And Reverse Strand Conventions
Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
Comment: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Answer: Details on salmon index
ATAC-seq sample normalization
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
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Recent Replies
Comment: BiomartException: Query ERROR for existing dataset in BioMart by Nyksubuz ▴ 10
The dataset you want (taestivum_eg_gene) exists within the "plants_mart" schema, not the default schema. Your current code assumes the defa…
Comment: Add line under stat test by Nyksubuz ▴ 10
You could use [this][1] [1]: https://ggplot2.tidyverse.org/reference/geom_segment.html
Comment: API kegg - IndexError: list index out of range by Nyksubuz ▴ 10
It might be because the gene symbol is not found in the KEGG database. Add some extra error handling before parsing the results or do a man…
Comment: Sam file Header problem by saifulislam99121 • 0
Thank you for your reply. I am not very much sure about this RG. Can you explain me a bit?
Comment: GRIDSS: the Genomic Rearrangement IDentification Software Suite by dario.garvan ▴ 520
It seems that Alexandrov's [structural variant and copy number signatures][1] estimated by the [SigProfiler software ecosystem][2] aren't c…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by GenoMax 142k
Then you may want to see if a program like `lastz` ([**LINK**][1]) may be useful. [1]: https://github.com/lastz/lastz
Comment: Collect dispersed executable files and run them by using bingo. by Ram 43k
What is the purpose of this tool? I have `~/bin` in my $PATH and I soft-link all executables I need to that location so why install a new t…
Comment: Merge clusters in Seurat UMAP by bk11 ★ 2.4k
Can you try this? library(dplyr) seuratobj@meta.data <- seuratobj@meta.data %>% mutate(seurat_clusters = recode(seurat_clu…
Comment: Merge clusters in Seurat UMAP by kilcdincer ▴ 10
Thank you for the response but it does not change anything.
Comment: Merge clusters in Seurat UMAP by bk11 ★ 2.4k
I have not tested but you could try something like below- seuratobj$seurat_clusters[seuratobj$seurat_clusters==5]=0 seuratobj$seur…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by Gabriel R. ★ 2.9k
I know about it, isn't there a simple C++ static binary?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by Gabriel R. ★ 2.9k
needle is great! but it does not handle sequences of 100k or so.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by Ram 43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction by txema.heredia ▴ 130
The point is that you need to feed the ambient algorithm a clustering list as input. This way, it checks for genes present in the soup vs g…
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by swbarnes2 14k
Wait, so the magnitudes of the PCs are in the thousands? That's not normal for RNASeq.
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