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794 results • Page 2 of 16
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6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma microarray DEA batch-effect
updated 29 days ago by 43k • written 4.7 years ago by ▴ 60
5
votes
7
replies
485
views
RNA seq analysis
DESeq RNA-seq
2 days ago by Jacek ▴ 20
5
votes
4
replies
722
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
2
replies
345
views
ChIP-seq datasets: input samples omitted?
ChIP-seq Normalization NGS
updated 18 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
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
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
5
votes
3
replies
314
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 17 days ago by ★ 1.2k • written 17 days ago by • 0
5
votes
5
replies
337
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA DADA2 metabarcoding
updated 14 days ago by ▴ 40 • written 15 days ago by ▴ 150
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
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
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 28 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
5
replies
663
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
6
replies
597
views
Programmatically retrieving positions of protein active site residues
Uniprot PDB Proteins
updated 16 days ago by ▴ 760 • written 17 days ago by ▴ 40
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
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
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
4
replies
2.9k
views
CNVkit for somatic copy number detection
cnv cnvkit exome WES
updated 3 days ago by • 0 • written 5.1 years ago by • 0
4
votes
2
replies
263
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 12 days ago by 43k • written 14 days ago by ▴ 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 9 days ago by ▴ 10 • written 2.5 years ago by • 0
4
votes
3
replies
194
views
Details on salmon index
Salmon
1 hour ago by Lorenzo • 0
4
votes
7
replies
633
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
373
views
Assume "yes" as the answer to any prompts with bioconda
docker container bioconda
updated 29 days ago by 8.6k • written 29 days ago by ▴ 20
4
votes
0
replies
159
views
Herald: The Biostar Herald for Monday, April 29, 2024
herald
18 days ago by Biostar 2.8k
4
votes
7
replies
604
views
To get p-values for the TPM
P-value TPM RSEM
updated 22 days ago by ★ 6.0k • written 23 days ago by • 0
4
votes
2
replies
271
views
How can I analyze normalized expression data?
DEseq2 RNA-seq
8 days ago by mnx0723 • 0
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
1
reply
255
views
LD-prune variants while maintaining a list of SNPs
snp vcf plink filtering independent
updated 11 days ago by 11k • written 12 days ago by ▴ 560
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
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
6
replies
802
views
7 follow
Heatmap and rna-seq
RNA-Seq Heatmap
updated 20 days ago by ★ 6.0k • written 24 days ago by ▴ 10
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome sequencing singleton SNP filter
updated 17 days ago by ▴ 20 • written 9.7 years ago by ▴ 40
4
votes
5
replies
4.3k
views
Tool: GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly Structural-Variation Variant-Calling
updated 13 hours ago by ▴ 520 • written 7.2 years ago by ★ 2.9k
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
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 8 days ago by 161k • written 8 days ago by ★ 1.2k
4
votes
7
replies
338
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA R VARIANCE
updated 11 minutes ago by ▴ 130 • written 1 day ago by ▴ 20
4
votes
2
replies
275
views
GRCh38.gmap file
gnomix gmap
12 days ago by lorena9132 ▴ 10
4
votes
5
replies
451
views
Figures are disappeared from html report of SnpEff
HTML SnpEff
18 days ago by analyst ▴ 50
4
votes
7
replies
409
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
3 days ago by Chen • 0
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
1
reply
355
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
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
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
11
replies
881
views
Redirection of Duplicate PMIDs
pubmed pmid
updated 23 days ago by 4.2k • written 24 days ago by • 0
4
votes
1
reply
200
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
2 days ago by J. ▴ 40
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
3
votes
3
replies
370
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 14 days ago by 82k • written 15 days ago by • 0
3
votes
0
replies
1.1k
views
Tool: Sars-Cov-2 Genome & ACE 2 Exploration
sequence alignment SNP genome
12 days ago by Ibrahim Tanyalcin ★ 1.2k
794 results • Page 2 of 16
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Comment: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: Details on salmon index
Answer: Generating consensus sequence from bam file
Answer: Short Read Data Genome Assembly
Comment: API kegg - IndexError: list index out of range
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Recent Replies
Comment: In one PCA plot, can I calculate the percentage of different factors that contri by marco.barr ▴ 130
great team work! why can't you access and do the calculation for the other components too? can't you extract the information from the other…
Comment: zero TPM for many gene including housekeeping when using kallisto by ATpoint 82k
Yes, but this is what I am saying: GAPDH in human has at least 6 annotated transcripts. Have you looked at all of them? Maybe that particul…
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint these are from PBMC. no they are different genes. for example ENST00000229239.10 is GAPDH. in STAR I got a lot of reads aligned …
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@dariober: I have to use kallisto for our downstream pipeline.
Comment: zero TPM for many gene including housekeeping when using kallisto by ATpoint 82k
Which celltype is this? Are these transcripts of the same gene, and of which gene?
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint the question is updated. the first command shows how the index is built.
Comment: Help! Reconstruction of locus, order contigs by dthorbur ★ 2.0k
Is the *de novo* annotation required for each contig? Reconstructing homologous regions in many genomes can be tricky regardless, but is es…
Comment: In one PCA plot, can I calculate the percentage of different factors that contri by diqixiaoyaoer ▴ 20
You can have a look on my answer. I have post it below.
Answer: In one PCA plot, can I calculate the percentage of different factors that contri by diqixiaoyaoer ▴ 20
Here is my script that can be used to calculate how much degree that different factors contribute to PCA variance (PC1 and PC2). # …
Comment: Details on salmon index by Lorenzo • 0
Thank you so much for the beautiful explanation. Just one more curiosity. So in the first versions Salmon utilized RapMap to index and then…
Comment: What marks a De-Novo Genome assembly as FAILED? by dthorbur ★ 2.0k
I'm a little confused about your experimental design. Are you making 45 different assemblies? Or are all the samples from the same individu…
Comment: zero TPM for many gene including housekeeping when using kallisto by ATpoint 82k
You should be stating how you constructed the index, and include the actual lines for the problematic genes from the abundance files. Note …
Comment: zero TPM for many gene including housekeeping when using kallisto by dariober 14k
You could try [salmon](https://combine-lab.github.io/salmon/getting_started/) to see if the problem is with kallisto or with the pseudo-ali…
Comment: solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* err by GenoMax 142k
> INPUT FILE error: could not open input file /geneInfo.tab Based on the error it appears that the input file you are providing could not …
Answer: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Having duplicate gene symbols is pretty common. Why do you need to work with gene symbols? To compare them to external datasets? Or just fo…
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