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735 results • Page 2 of 15
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5
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5
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672
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Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 14 days ago by • 0 • written 23 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 28 days ago by 82k • written 29 days ago by ★ 1.7k
5
votes
5
replies
349
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA DADA2 metabarcoding
updated 16 days ago by ▴ 40 • written 16 days ago by ▴ 150
5
votes
3
replies
321
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 18 days ago by ★ 1.2k • written 18 days ago by • 0
5
votes
6
replies
606
views
Programmatically retrieving positions of protein active site residues
Uniprot PDB Proteins
updated 17 days ago by ▴ 760 • written 19 days ago by ▴ 40
5
votes
2
replies
439
views
Missing protein (VEGF-A) in String db
VGFA stringdb
updated 22 days ago by ▴ 10 • written 3 months ago by ▴ 20
4
votes
1
reply
258
views
LD-prune variants while maintaining a list of SNPs
snp vcf plink filtering independent
updated 12 days ago by 11k • written 13 days ago by ▴ 560
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 9 days ago by 161k • written 9 days ago by ★ 1.2k
4
votes
2
replies
270
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 13 days ago by 43k • written 15 days ago by ▴ 40
4
votes
0
replies
159
views
Herald: The Biostar Herald for Monday, April 29, 2024
herald
19 days ago by Biostar 2.8k
4
votes
7
replies
635
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
19 days ago by e.r.zakiev ▴ 210
4
votes
8
replies
772
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs BED eqtl bedtools
updated 21 days ago by 35k • written 22 days ago by ▴ 10
4
votes
1
reply
204
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
4 days ago by J. ▴ 40
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 10 days ago by ▴ 10 • written 2.5 years ago by • 0
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference 38build impute imputation
18 days ago by anna ▴ 20
4
votes
2
replies
276
views
How can I analyze normalized expression data?
DEseq2 RNA-seq
9 days ago by mnx0723 • 0
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
2
replies
282
views
GRCh38.gmap file
gnomix gmap
13 days ago by lorena9132 ▴ 10
4
votes
7
replies
425
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
4 days ago by Chen • 0
4
votes
7
replies
611
views
To get p-values for the TPM
P-value TPM RSEM
updated 23 days ago by ★ 6.0k • written 24 days ago by • 0
4
votes
4
replies
3.0k
views
CNVkit for somatic copy number detection
cnv cnvkit exome WES
updated 4 days ago by • 0 • written 5.1 years ago by • 0
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 15 days ago by • 0 • written 2.2 years ago by • 0
4
votes
9
replies
428
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch alignment
1 day ago by Gabriel R. ★ 2.9k
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome sequencing singleton SNP filter
updated 18 days ago by ▴ 20 • written 9.7 years ago by ▴ 40
4
votes
6
replies
808
views
7 follow
Heatmap and rna-seq
RNA-Seq Heatmap
updated 21 days ago by ★ 6.0k • written 25 days ago by ▴ 10
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 14 days ago by ★ 7.2k • written 5 months ago by ▴ 10
4
votes
5
replies
4.4k
views
Tool: GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly Structural-Variation Variant-Calling
updated 1 day ago by ▴ 520 • written 7.2 years ago by ★ 2.9k
4
votes
3
replies
442
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc conda nextflow
updated 20 days ago by 3.2k • written 21 days ago by ▴ 40
4
votes
11
replies
888
views
Redirection of Duplicate PMIDs
pubmed pmid
updated 24 days ago by 4.2k • written 25 days ago by • 0
4
votes
12
replies
4.9k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation Experience Illumina Mouse
updated 9 days ago by ▴ 180 • written 3.0 years ago by ▴ 20
4
votes
7
replies
465
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA R VARIANCE
updated 1 day ago by ▴ 130 • written 3 days ago by ▴ 20
4
votes
5
replies
455
views
Figures are disappeared from html report of SnpEff
HTML SnpEff
19 days ago by analyst ▴ 50
4
votes
1
reply
358
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma voom R
18 days ago by pairedttest ▴ 10
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq RNA-Seq exon
updated 12 days ago by ▴ 30 • written 6.7 years ago by ★ 1.2k
4
votes
2
replies
3.8k
views
DESeq2 design and batch effect
RNA-Seq batch-effect DESeq2 Salmon
updated 29 days ago by 43k • written 6.6 years ago by ▴ 30
4
votes
5
replies
3.4k
views
How to compare compare two Sam files to check mapping
alignment
updated 10 days ago by ▴ 90 • written 6.4 years ago by ▴ 60
3
votes
3
replies
371
views
Sequence read length shorter than flow cell specification
illumina NGS sequencing
updated 22 days ago by 14k • written 23 days ago by • 0
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 10 days ago by • 0 • written 5.6 years ago by 8.5k
3
votes
3
replies
284
views
what is another word for a BLAST "hit"?
blast alignment
7 days ago by dec986 ▴ 380
3
votes
8
replies
605
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
11 days ago by Qroid ▴ 40
3
votes
4
replies
753
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
26 days ago by rahu • 0
3
votes
3
replies
271
views
Gene Specific coverage from WGS data
WGS SARS-CoV2
updated 4 days ago by 43k • written 18 days ago by • 0
3
votes
3
replies
3.0k
views
Quick way to Identify batch effect from covariates?
bioconductor batch-effect
updated 29 days ago by 43k • written 8.0 years ago by ★ 3.4k
3
votes
1
reply
236
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 3 days ago by 14k • written 4 days ago by ▴ 30
3
votes
2
replies
317
views
p-value and Boneferroni adjusted p-value the same in R
Bonferroni R Statistics p-value Fisher
26 days ago by kristiewyleung • 0
3
votes
5
replies
642
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align RNA-Seq linux STAR
26 days ago by n_navy • 0
3
votes
3
replies
378
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression RNA NOISeq DGE
updated 15 days ago by 82k • written 16 days ago by • 0
3
votes
5
replies
404
views
Converting CRAM to FastQ
GATK samtools cram SamToFastq fastq
14 days ago by Maverick ▴ 10
3
votes
2
replies
286
views
imputation through beagle
panel beagle reference imputation
4 days ago by analyst ▴ 50
3
votes
2
replies
4.2k
views
Batch effects in sequencing data
batch-effect
updated 29 days ago by 43k • written 8.8 years ago by ▴ 60
735 results • Page 2 of 15
Recent Votes
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
Answer: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
C: How can I perform Differential expression analysis with just one control and one
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Recent Replies
Comment: constructing pangenome through psvcp by analyst ▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by GenoMax 142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R by 1769mkc ★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks by ATpoint 82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner by Joe 21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression? by Gordon Smyth ★ 7.2k
See the exploration of isoform precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Table 1 o…
Comment: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA by mavy ▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object by Alex Reynolds 35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF) by aidangcruickshank ▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data? by Ngrin • 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2 by swbarnes2 14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot by LauferVA 4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
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