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547 results • Page 2 of 11
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1
vote
1
reply
1.7k
views
sea corrected expression matrix
sva microarrays batch-effect
updated 7 days ago by 43k • written 6.8 years ago by ▴ 380
0
votes
0
replies
1.7k
views
Differential Gene Expression Analysis using two distinct scRNA-seq datasets
differential-gene-expression RNA-Seq scRNA-seq
updated 14 days ago by 43k • written 6.5 years ago by ▴ 120
0
votes
0
replies
1.7k
views
Batch effect and CCA
CCA RNA-Seq seurat batch-effect
updated 6 days ago by 43k • written 5.1 years ago by ▴ 110
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma microarray DEA batch-effect
updated 6 days ago by 43k • written 4.7 years ago by ▴ 60
0
votes
5
replies
1.6k
views
what does mean this error ? "(ERR): hisat2-align exited with value 1" in mapping long noncoding RNAs
long-non-coding-RNA lncRNA
updated 18 days ago by 43k • written 2.6 years ago by • 0
2
votes
2
replies
1.6k
views
read count for RNA sequencing via nanopore
long-reads RNA-seq gene-expression read-count
updated 18 days ago by 43k • written 2.9 years ago by • 0
1
vote
6
replies
1.6k
views
How can Differentially Expressed Genes be found by limma package after removing batch effect by ComBat function in sva package?
limma sva batch-effect R
updated 8 days ago by 43k • written 3.8 years ago by ▴ 10
2
votes
18
replies
1.6k
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome phg_v2 plants PHG
22 days ago by b.contreras.moreira ▴ 170
2
votes
5
replies
1.6k
views
Adding functional annotation and meta-data of MAKER/BRAKER GFF
metadata functional-annotation BRAKER MAKER
updated 22 days ago by ▴ 40 • written 15 months ago by ▴ 60
2
votes
3
replies
1.5k
views
Duplicate row name not allowed while reading the file in R
RNA-Seq deseq2 Differential-Gene-expression R
updated 14 days ago by 43k • written 4.9 years ago by • 0
0
votes
0
replies
1.5k
views
RIPSeeker viewRIP function fails to extract values() in GRangesList/S4 object
RIPSeq S4 RIP R
updated 7 days ago by 43k • written 6.2 years ago by ▴ 80
0
votes
0
replies
1.5k
views
minifi for RRBS
rrbs batch-effect methylation
updated 7 days ago by 43k • written 7.1 years ago by ★ 2.9k
0
votes
0
replies
1.4k
views
Help with Circos plot "Assumption Error" that prevents plotting a protein interactions network
CircosPlot
updated 7 days ago by 43k • written 3.3 years ago by • 0
2
votes
4
replies
1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray combat batch-effect median-normalization
updated 5 days ago by 43k • written 18 months ago by • 0
1
vote
4
replies
1.3k
views
Splitting long reads into shorter chunks
long-read
updated 18 days ago by 43k • written 5.8 years ago by ▴ 60
0
votes
0
replies
1.3k
views
which value from ruvadj in missMethyl can present methylation status
R RUV methylation missmethyl batch-effect
updated 7 days ago by 43k • written 6.0 years ago by ▴ 20
0
votes
1
reply
1.3k
views
About BatchQC packages error
Batch-effect R
updated 6 days ago by 43k • written 6.1 years ago by • 0
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq batch-effect DESeq2
updated 6 days ago by 43k • written 4.4 years ago by ▴ 10
0
votes
1
reply
1.2k
views
Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
random-effects RNA-Seq batch-effect
updated 7 days ago by 43k • written 6.8 years ago by • 0
0
votes
1
reply
1.2k
views
Controlling for batch effect in SNP-based PCA
whole-genome PCA batch-effect SNP
updated 6 days ago by 43k • written 4.7 years ago by ▴ 90
0
votes
0
replies
1.2k
views
Batch estimate using kBET
batch-effect kbet
updated 5 days ago by 43k • written 4.0 years ago by • 0
0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling single-cell scRNA-seq batch-effect
updated 7 days ago by 43k • written 3.9 years ago by ▴ 20
0
votes
5
replies
1.2k
views
RNAseq differential gene expression analysis yield results which come from digestive content
differential-gene-expression RNA-Seq
updated 14 days ago by 43k • written 6.4 years ago by ▴ 90
0
votes
0
replies
1.1k
views
Extra adjustment variables during batch effect correction
rna-seq ComBat batch-effect
updated 7 days ago by 43k • written 4.3 years ago by ▴ 360
2
votes
3
replies
1.1k
views
Polishing PACBIO corrected assembly using ONT and ILLUMINA data (.fastq)
fasta Nanopore long-read fastq
updated 18 days ago by 43k • written 2.8 years ago by ▴ 10
0
votes
3
replies
1.1k
views
Batch effect for SNP array
sva combat batch-effect SNP
updated 8 days ago by 43k • written 4.2 years ago by ▴ 10
0
votes
4
replies
1.1k
views
Getting biological replicates from SRA run NCBI
fastq AWS SRA RNAseq
22 days ago by Andres ▴ 20
0
votes
0
replies
1.1k
views
Should batch correction be performed before or after feature selection in scRNA-seq
batch-effect scRNA-seq feature-selection
updated 6 days ago by 43k • written 4.9 years ago by ▴ 140
0
votes
1
reply
1.1k
views
Ensembl assembly choice for RNA-Seq reference mapping
RNA-Seq ensembl STAR alignment Assembly
updated 12 days ago by ▴ 20 • written 5.0 years ago by ▴ 30
0
votes
0
replies
1.1k
views
Effect of dbSNP build differences in variant calling
GRCh38 dbSNP variant-calling GATK assembly
updated 28 days ago by 43k • written 5.4 years ago by ▴ 30
0
votes
0
replies
1.1k
views
Finding wobble/redundant positions in an RNA string using R.
RNA wobble-position R
updated 7 days ago by 43k • written 6.2 years ago by ▴ 100
0
votes
0
replies
1.1k
views
Isoforms or Duplications
Differential-Gene-Expression RNA-Seq
updated 14 days ago by 43k • written 7.1 years ago by ▴ 10
1
vote
0
replies
1.0k
views
interpretation of trajectory and batch effect
monocle3 batch-effect trajectory
updated 15 days ago by 43k • written 3.5 years ago by ▴ 10
1
vote
2
replies
1.0k
views
An issue with application of SPAdes genome assembly in Galaxy
Galaxy SPAdes
updated 21 days ago by 43k • written 2.4 years ago by • 0
0
votes
6
replies
1.0k
views
Considering that the basal expression level is not 0 for the calculation of the differential expression
DESEQ2 RNA-Seq Differential-gene-Expression
updated 14 days ago by 43k • written 5.7 years ago by ▴ 340
0
votes
2
replies
1.0k
views
proportional hazard assumption was not satisfied for a covariate
hazard-ratios Cox-model survival
updated 7 days ago by 43k • written 4.4 years ago by ▴ 40
2
votes
1
reply
951
views
How to evaluate the performance of an RNA-seq pipeline
Differential-gene-expression RNA-Seq R DESeq2
updated 14 days ago by 43k • written 4.0 years ago by ▴ 300
2
votes
3
replies
926
views
Possible approach to select normal tissue samples for cancer RNA-Seq data without reference data for downstream analyses
R RNA-Seq DE batch-effect GTEx
updated 8 days ago by 43k • written 4.1 years ago by ▴ 790
1
vote
2
replies
917
views
vg surject for long reads
long-reads vg variation-graph surject
updated 18 days ago by 43k • written 23 months ago by ▴ 10
0
votes
0
replies
888
views
Advice on group specific condition effect and model matrix in deseq2
deseq2 batch-effect
updated 8 days ago by 43k • written 4.1 years ago by ▴ 330
1
vote
7
replies
882
views
GATK Mutect2 Input files reference and features have incompatible contigs: No overlapping contigs found.
hg19 Mutect2 GATK Variant-Calling
updated 28 days ago by 43k • written 9 months ago by ▴ 100
0
votes
0
replies
871
views
Variant quality scores with different variant caller: HaplotypeCaller vs DeepVariant. How to interpret the quality scores?
variant-calling DeepVariant HaplotypeCaller quality-score
updated 28 days ago by 43k • written 2.5 years ago by ▴ 50
0
votes
2
replies
867
views
freebayes calls presumably homozygous variants as heterozygotes
SNP freebayes variant-call genotyping
updated 18 days ago by • 0 • written 3.1 years ago by • 0
2
votes
6
replies
856
views
Batch effect correction with cell type enrichment analysis
limma RNA-seq r batch-effect
updated 7 days ago by 43k • written 19 months ago by ▴ 140
4
votes
13
replies
842
views
RNAseq of primary tumor and metastases in two different organ
metastases RNA-seq DEG R
updated 7 days ago by ★ 1.7k • written 12 days ago by • 0
0
votes
0
replies
841
views
Estimating sequence complexity of DNA sequence from fasta file
sequence RepeatMasker pacbio
updated 7 days ago by 43k • written 5.6 years ago by ▴ 10
4
votes
6
replies
830
views
bwa mem hangs after a few thousand reads
bwa alignment variant-calling bwa-mem
updated 21 days ago by 43k • written 4 months ago by ▴ 30
0
votes
1
reply
829
views
How to compare differentially expressed genes among different affymatrix dataset
microarray batch-effect R
updated 6 days ago by 43k • written 4.8 years ago by ▴ 30
1
vote
2
replies
820
views
Replacing default numbers with geneNames in enhancedVolcano
EnhancedVolcano
updated 21 days ago by 43k • written 2.6 years ago by • 0
0
votes
1
reply
815
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR Batch-effect RNA-Seq
updated 5 days ago by 43k • written 3.7 years ago by • 0
547 results • Page 2 of 11
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Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
C: RSeQC Output from infer_experiment.py - what does it mean?
Read pair orientation : Illumina TruSeq Stranded mRNA library
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Recent Replies
Comment: To get p-values for the TPM by dsull ★ 5.8k
Your post should be a "com, not an "answer". Use "Add Comment" to request clarifications on an answer someone has provided. tximport can t…
Comment: Use of Kraken output for functional analysis by gv • 0
Hello, you can use kraken-biom [kraken_biom.py] tool to get your Biom file from input kreport cheers,
Answer: To get p-values for the TPM by VITALA • 0
sir, deseq2 takes counts as inputs rightfor the hypothesis testing /to see the variance between the two groups, but in my case what i want …
Answer: To get p-values for the TPM by dsull ★ 5.8k
There are plenty of RSEM -> tximport -> DESeq2 tutorials online. Just follow one of those. DESeq2 will give you "p values" based on a Wa…
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File? by dsull ★ 5.8k
I agree for the most part. However, Heng Li has argued that the one application that they are essential for is short read variant calling. …
Comment: interpretartion of a vcf file by samuelkalandarov2002 ▴ 10
In my case , there is only one sample : here is an example of a some variants generated using minipileup : #CHROM POS ID REF ALT QUAL FI…
Comment: How to calculate identity percentage between proteins contained in a FASTA file? by b.contreras.moreira ▴ 170
This should work if you know your sequences are related and can be globally aligned; otherwise it is safer to compute local alignments (for…
Comment: How to compare the quality of assemblies by kirillkirilenko ▴ 40
A haploid assembly is our goal. For purging we used prefix.p_ctg.gfa (assembly graph of primary contigs).
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File? by Istvan Albert 100k
What I mean is that no sequencing run can be calibrated with the claimed precision. Where it could correctly distinguish between basecalls …
Comment: HaplotypeCaller - only SNPs by analyst ▴ 20
After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file ([link to command][1]) [1]: https://gatk…
Comment: GTF file for Rhinolophus sinicus by atowns21 • 0
Ah gotcha. I guess what doesn't make sense to me is why a [paper][1] published in 2022 uses that reference genome. [1]: https://www.na…
Answer: Wilcox test using data slot (log normalized count values) of scRNA-seq between t by yxwucq • 0
The best way is to generate a pseudo-bulk aggregation then apply edgeR or DESeq2. You can also directly use wilcoxon on sc-level, since man…
Comment: How to solve this RoseTTAFold colaboratory error? by Mensur Dlakic ★ 27k
There is a dedicated Discord group that deals with everything related to ColabFold and its derivatives. Below is an invitation to join that…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by atowns21 • 0
Hmm, okay I'm not sure what is going on, but here is what I did: 1. Downloaded a single fastq: `parallel-fastq-dump --tmpdir . --threads …
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks? by HyperEvo • 0
Ok, thank you so much~
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