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1,000 results • Page 4 of 20
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3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression Salmon
updated 14 days ago by 43k • written 5.5 years ago by ▴ 100
3
votes
6
replies
8.3k
views
RNA-seq, EdgeR and batch effects
RNA-Seq removeBatchEffect edgeR batch-effect
updated 7 days ago by 43k • written 9.3 years ago by ▴ 120
7
votes
6
replies
440
views
Filtering sam or bam file with maximum matching region
crisper-edited alignment match
3 days ago by analyst ▴ 30
2
votes
6
replies
561
views
Hybrid assembly Pacbio- Nanopore
long-reads hybric assembly genome short-reads
19 days ago by Lissa Cruz Saavedra • 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
3
votes
6
replies
2.4k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq combat rna-seq sva batch-effect
updated 7 days ago by 43k • written 21 months ago by ▴ 20
0
votes
6
replies
451
views
Error in running Mauve alignner in Ubuntu 20.04
java linux aligner mauve
14 days ago by marongiu.luigi ▴ 710
1
vote
6
replies
399
views
Rename multiple fastq.gz files
fastq next-gen
updated 7 days ago by 8.4k • written 7 days ago by • 0
2
votes
6
replies
393
views
create a gene count matrix csv file from seurat object
Seurat sparseMatrix
15 days ago by jkim ▴ 170
3
votes
6
replies
4.0k
views
Loading previously downloaded GEO SOfT data into R, using getGEO from GEOquery package
microarray r GEOquery
updated 7 days ago by 43k • written 5.0 years ago by ▴ 30
3
votes
6
replies
621
views
Ciriquant not configuring hisat2 indexed files
ciriquant
2 days ago by Atul K. • 0
11
votes
6
replies
509
views
Pangenome of plant
pangenome plant
16 days ago by analyst ▴ 30
0
votes
6
replies
276
views
How to slice a gvcf file with tabix?
Tabix bed gvcf
20 hours ago by Sd • 0
8
votes
6
replies
2.5k
views
Batch effect removal with the help of sva
SVA batch-effect gene-expression
updated 15 days ago by 43k • written 3.5 years ago by ▴ 240
5
votes
6
replies
387
views
7 follow
Seeking Help with Unexpected MA Plot Output
MAplot RNAseq Rstudio
updated 22 days ago by 100k • written 22 days ago by • 0
0
votes
6
replies
612
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
differential-expression RNA-Seq ONT Nanopore
updated 14 days ago by 43k • written 4 months ago by • 0
2
votes
6
replies
857
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
2
votes
6
replies
626
views
Overlapping and merging ChIP-seq peaks
MACS2 HOMER ChIP-seq peak-calling
updated 22 days ago by 43k • written 4 months 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
7
votes
6
replies
1.3k
views
using different microarray datasets (meta-analysis?) for DEG pipeline
microarray meta-analysis DEG batch-effect
updated 6 days ago by 43k • written 4.8 years ago by ▴ 30
1
vote
6
replies
2.1k
views
DGE on protein-coding and lncRNAs separately?
differential-gene-expression RNA-seq
updated 14 days ago by 43k • written 6.5 years ago by ★ 1.6k
2
votes
6
replies
3.7k
views
Algorithm to remove batch effects
single-cell batch-effect RNA-Seq
updated 7 days ago by 43k • written 3.3 years ago by ▴ 80
0
votes
6
replies
539
views
PacBio adapters in transcriptome assembly from short read data?
adapter transcriptome sequencing pacbio vecscreen
8 days ago by Dunois ★ 2.5k
2
votes
6
replies
502
views
Correcting coordinates in gff3 file
awk unix gff3 python
updated 12 days ago by 4.5k • written 14 days ago by • 0
4
votes
6
replies
3.9k
views
Correcting for batch effect in RNA-seq data
RNA-Seq batch-effect
updated 6 days ago by 43k • written 4.8 years ago by ▴ 30
3
votes
6
replies
1.5k
views
edgeR FDR always 1
FDR differential-gene-expression edgeR miRNA
updated 14 days ago by 43k • written 4.9 years ago by ▴ 20
1
vote
6
replies
2.5k
views
Variant calling from multiple sequencing runs for a single samples
variant-calling
updated 29 days ago by 43k • written 7.0 years ago by • 0
2
votes
6
replies
444
views
KEGG analysis in R
KEGG clusterProfiler Zea-mays
12 days ago by sansan_96 ▴ 80
4
votes
6
replies
1.4k
views
CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRleFromGR(x, weight = weight, ignore.strand = ignore.strand): Seqlength…
gff3 GenomicRanges ORFik GenomicFeatures
updated 9 days ago by 141k • written 14 months ago by ▴ 30
5
votes
6
replies
7.3k
views
scatter plot, aov()
aov scatter-plot anova
updated 7 days ago by 43k • written 3.1 years ago by ▴ 170
4
votes
6
replies
440
views
Odd results with BLAST remote
blast remote NCBI
updated 8 days ago by ▴ 170 • written 9 days ago by ▴ 150
15
votes
6
replies
1.3k
views
6 follow
VCF to human friendly form?
vcf visualization
updated 9 days ago by 161k • written 19 months ago by ▴ 10
4
votes
6
replies
831
views
bwa mem hangs after a few thousand reads
bwa alignment variant-calling bwa-mem
updated 22 days ago by 43k • written 4 months ago by ▴ 30
0
votes
6
replies
415
views
Use of Kraken output for functional analysis
metagenomics kraken shotgun
updated 6 hours ago by • 0 • written 23 days ago by ▴ 20
10
votes
6
replies
4.1k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 28 days ago by 43k • written 6.2 years ago by 87k
1
vote
6
replies
429
views
Coverage depth map of genome from multiple sample coverage bedgraphs?
bedops bedmap coverage
29 days ago by Agastya ▴ 10
3
votes
6
replies
11k
views
List of species in RepeatMasker Tool (species parameter)
RepeatMasker Masking
updated 7 days ago by ▴ 10 • written 7.6 years ago by ▴ 10
2
votes
6
replies
3.4k
views
Base Quality of a reported variant in VCF
alignment FASTQ VCF next-gen Variant-Calling
updated 29 days ago by 43k • written 9.2 years ago by ▴ 50
9
votes
6
replies
1.5k
views
What in silico PCR commandline tool do you use that can handle IUPAC characters?
pcr amplicon primer
updated 22 days ago by 43k • written 16 months ago by ▴ 710
8
votes
6
replies
608
views
The bioinformatics paper reappears, but the results are significantly different from the original results
reproducibility
19 days ago by jiao ▴ 40
4
votes
6
replies
2.0k
views
RNA-Seq DGE: Evaluate model quality
differential-gene-expression RNA-Seq deseq2
updated 14 days ago by 43k • written 6.2 years ago by ★ 1.6k
2
votes
6
replies
5.2k
views
How to avoid over-correction by using harmony or CCA to batch correction in scRNA-seq?
scRNA-seq R seurat harmony batch-effect
updated 5 days ago by 43k • written 3.7 years ago by • 0
2
votes
5
replies
501
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis MEGA
updated 3 days ago by ★ 27k • written 4 days ago by • 0
2
votes
5
replies
2.8k
views
Batch effect in Axiom Human Origins Array
affymetrix array batch-effect
updated 7 days ago by 43k • written 7.9 years ago by ▴ 50
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython PDB Radius of Gyration python protein
updated 4 days ago by • 0 • written 6.5 years ago by ▴ 30
2
votes
5
replies
425
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats hg002 bed homopolymer-regions
7 days ago by Bikram Kumar • 0
3
votes
5
replies
526
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align RNA-Seq linux STAR
2 days ago by n_navy • 0
0
votes
5
replies
1.8k
views
Demultiplexing multiple amplicons from one fastq based on primer sequence
demultiplexing illumina
updated 15 days ago by 3.2k • written 3.4 years ago by • 0
3
votes
5
replies
651
views
somatic variant calling without matched normal in long-reads
variants cancer illumina ONT nanopore
29 days ago by eesiribloom ▴ 80
5
votes
5
replies
842
views
Blacklist for bacterial genome [ChIPseq]?
ChIPseq Blacklist
updated 11 days ago by 43k • written 10 months ago by ▴ 30
1,000 results • Page 4 of 20
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Recent Replies
Comment: How to convert plink files to Hapmap Format by bk11 ★ 2.3k
Please show me a few lines of phenotype updated .fam file. You can do `head your_data_phenoUP.fam` and paste result here. Please do not us…
Comment: GEMMA GWAS how to specify factor or numerical for covariates by Sofia • 0
Hi, I don't have a solution to your question but I followed this tutorial and was helpful to me in my analysis https://youtu.be/NusV6duyvXs…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas by GenoMax 141k
Catalog file lists the genomes included. There seem to be 71365 unique items in field 2. 2 Bacteria WP_000018326.1 4459…
Comment: How to convert plink files to Hapmap Format by Sofia • 0
yes sure ! ![enter image description here][1] [1]: /media/images/f0f94f6c-4387-4188-a1aa-19152a89
Answer: AGeNT LocatIt by Greg • 0
Give it more memory. ~10x more memory, or whatever you can give it, I had samples that weren't even close to being done after 3.5 da…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas by Bertalan_Takacs ▴ 90
Thanks! I've already tried looking through these files, I need release 83. I am trying to find this information in the .catalog file of the…
Answer: Is it possible to get a list of representative genomes from a past RefSeq releas by GenoMax 141k
Possibly. You will need to know the RefSeq release version. Check in this directory: https://ftp.ncbi.nlm.nih.gov/refseq/release/release-ca…
Comment: How to convert plink files to Hapmap Format by bk11 ★ 2.3k
Hey, can you please show me a few lines of your phenotype updated .fam file? I m seeing there are 7 columns in it, that might be the proble…
Comment: PCA plot (Suggestions Needed) by jkim ▴ 170
How much variance were explained by PC1 and PC2? It doesn't look like that the largest source of variation came from the genotype differenc…
Comment: How to trim transcripts using information from NCBI contamination screen report by Lada ▴ 30
Thank you and yes, I agree going step back is the best option but I am in a hurry at the moment so I just need to stick to the transcriptom…
Comment: How to convert plink files to Hapmap Format by Sofia • 0
Thank you so much for helping me out! I did the steps you mentioned but still got the same issue as shown in the snapshot ![enter image des…
Comment: different FeatureCounts output for the same data by Istvan Albert 100k
Make sure you are using the same version of featureCounts, it has changed how it deals with paired end reads. The exact same command will p…
Comment: Wilcox test using data slot (log normalized count values) of scRNA-seq between t by mropri ▴ 150
Thank you, will do Wilcox for now as I only have one control and one treatment, as I get more control and treatment samples, will stick wit…
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File? by Istvan Albert 100k
I think the blog post lines up wit both of our statements. It seems that 2-way binning (pass/fail) already dramatically improves the calls…
Comment: Tax4Fun2 - error by drstalinantony28 • 0
You have to follow this step to solve the issue. (Mostly this problem occurs in the Windows version) 1. If you are using R studio in Windo…
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