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506 results • Page 1 of 11
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13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva combat batch-effect
updated 1 day ago by 43k • written 6.8 years ago by ★ 1.3k
11
votes
22
replies
4.1k
views
No significant DEG: A request to double check my commands for limma.
limma differential-gene-expression
updated 8 days ago by 43k • written 5.0 years ago by ▴ 260
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
16 days ago by b.contreras.moreira ▴ 150
4
votes
13
replies
749
views
RNAseq of primary tumor and metastases in two different organ
metastases RNA-seq DEG R
updated 1 day ago by ★ 1.7k • written 7 days ago by • 0
2
votes
12
replies
689
views
Nanopore data filtering using fastp
fastp nanopore
20 days ago by emilydolivo97 ▴ 10
3
votes
12
replies
473
views
struggle to get fasta files from ucsc goldenPath
ucsc getfasta fasta
16 days ago by Lila M ★ 1.2k
4
votes
12
replies
3.5k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling samtools VCF BCF
updated 23 days ago by 43k • written 5.5 years ago by ▴ 110
2
votes
10
replies
784
views
Only one read per run - Trying to use CellRangerv7
Fastq CellRanger
updated 21 days ago by 43k • written 8 weeks ago by ▴ 10
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 1 day ago by 43k • written 7.4 years ago by • 0
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma microarray DEA batch-effect
updated 22 hours ago by 43k • written 4.7 years ago by ▴ 60
8
votes
10
replies
646
views
bash script
whole-genome-sequencing
updated 2 days ago by 43k • written 10 days ago by ▴ 30
0
votes
10
replies
579
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
17 days ago by dzisis1986 ▴ 70
0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling single-cell scRNA-seq batch-effect
updated 1 day ago by 43k • written 3.9 years ago by ▴ 20
4
votes
9
replies
540
views
variant calling
variant-calling
updated 15 days ago by 43k • written 16 days ago by • 0
0
votes
9
replies
542
views
99.9999% of Q30 bases is normal?
RNA-seq fastp
updated 6 days ago by 4.2k • written 7 days ago by ▴ 10
0
votes
9
replies
459
views
Low number of both surviving reads after trimming
trimmomatic trimming
20 days ago by Jay • 0
5
votes
8
replies
3.6k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression RNA-seq gene-ontology
updated 8 days ago by 43k • written 6.5 years ago by ★ 1.6k
0
votes
8
replies
5.2k
views
8 follow
cellranger mkref failed
next-gen-sequencing software-error RNA-seq
updated 8 days ago by • 0 • written 4.7 years ago by ▴ 180
0
votes
8
replies
499
views
STAR aligner options
STAR
21 days ago by theophile • 0
1
vote
8
replies
3.4k
views
Best way to address different batches of RNA-seq
sequence RNA-Seq RPKM Fold-Change batch-effect
updated 22 hours ago by 43k • written 7.0 years ago by ▴ 20
0
votes
7
replies
379
views
DESeq: too low p-value for RNAseq
R DESeq p-value RNA-seq FDR
updated 13 days ago by ★ 2.9k • written 14 days ago by ▴ 10
0
votes
7
replies
6.0k
views
Pre-processing of RNA-Seq data for WGCNA
RNA-Seq WGCNA removeBatchEffect DESeq2
updated 1 day ago by 43k • written 7.6 years ago by ▴ 70
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression RNA-Seq GTex DESeq2
updated 8 days ago by 43k • written 6.4 years ago by ▴ 10
4
votes
7
replies
538
views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
JBrowse JBrowse2
updated 16 days ago by ★ 3.8k • written 19 days ago by ▴ 140
4
votes
7
replies
2.3k
views
Batch effects vs biological variables
Batch-effect DESeq2 combat_seq
updated 9 days ago by 43k • written 3.7 years ago by ▴ 20
0
votes
7
replies
389
views
Salmon Quantification in Alignment based-mode
Salmon RNA-seq TPM
updated 21 days ago by 141k • written 22 days ago by • 0
1
vote
7
replies
878
views
GATK Mutect2 Input files reference and features have incompatible contigs: No overlapping contigs found.
hg19 Mutect2 GATK Variant-Calling
updated 23 days ago by 43k • written 8 months ago by ▴ 100
4
votes
7
replies
521
views
DESeq2 Multifactor Design
RNA-seq DESeq2
updated 4 days ago by 43k • written 5 days ago by ▴ 20
1
vote
6
replies
495
views
Quest about the input data for PCA analysis
PCA
26 days ago by tujuchuanli ▴ 100
4
votes
6
replies
822
views
bwa mem hangs after a few thousand reads
bwa alignment variant-calling bwa-mem
updated 16 days ago by 43k • written 4 months ago by ▴ 30
2
votes
6
replies
845
views
Batch effect correction with cell type enrichment analysis
limma RNA-seq r batch-effect
updated 1 day ago by 43k • written 18 months ago by ▴ 140
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 8 days ago by 43k • written 5.7 years ago by ▴ 340
0
votes
6
replies
507
views
PacBio adapters in transcriptome assembly from short read data?
adapter transcriptome sequencing pacbio vecscreen
2 days ago by Dunois ★ 2.5k
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 2 days ago by 43k • written 3.8 years ago by ▴ 10
2
votes
6
replies
618
views
Overlapping and merging ChIP-seq peaks
MACS2 HOMER ChIP-seq peak-calling
updated 16 days ago by 43k • written 4 months ago by • 0
2
votes
6
replies
535
views
Removing duplicates
duplicates ONT minimap2
7 hours ago by quentinperriere • 0
3
votes
6
replies
2.4k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq combat rna-seq sva batch-effect
updated 1 day ago by 43k • written 21 months ago by ▴ 20
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression Salmon
updated 8 days ago by 43k • written 5.5 years ago by ▴ 100
2
votes
6
replies
372
views
create a gene count matrix csv file from seurat object
Seurat sparseMatrix
9 days ago by jkim ▴ 170
0
votes
6
replies
607
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
differential-expression RNA-Seq ONT Nanopore
updated 8 days ago by 43k • written 4 months ago by • 0
0
votes
6
replies
442
views
Download Panther entry list
PANTHER
27 days ago by Nicolas • 0
2
votes
6
replies
507
views
Need help understanding core SNPs
SNPs snippy
24 days ago by ujichu • 0
0
votes
6
replies
434
views
Error in running Mauve alignner in Ubuntu 20.04
java linux aligner mauve
8 days ago by marongiu.luigi ▴ 710
5
votes
6
replies
380
views
7 follow
Seeking Help with Unexpected MA Plot Output
MAplot RNAseq Rstudio
updated 15 days ago by 100k • written 16 days ago by • 0
3
votes
5
replies
390
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
updated 15 days ago by 141k • written 15 days ago by ▴ 190
0
votes
5
replies
309
views
Incongruencies in GT assignment by Freebayes
depth freebayes heterozygous genotype
13 days ago by virginia.baraja • 0
0
votes
5
replies
360
views
Parsing fasta file by coordinates
linux fasta
updated 20 days ago by 141k • written 23 days ago by ▴ 120
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 8 days ago by 43k • written 6.4 years ago by ▴ 90
0
votes
5
replies
357
views
Use of Kraken output for functional analysis
metagenomics kraken shotgun
14 days ago by Srinka ▴ 20
0
votes
5
replies
2.0k
views
Batch effect correction & normalization after training/test split for gene expression data
RNA-seq batch-effect normalization
updated 1 day ago by 43k • written 20 months ago by ▴ 60
506 results • Page 1 of 11
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A: Best strategy for gene annotation for de novo genome assembly without RNA-seq da
Comment: Questions about a bug when transferring cram file to bam file
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Comment: Trying to write bwa mem -> samtools view -> samtools sort loop
C: Extract fasta sequences from a file using a list in another file.
A: Extract fasta sequences from a file using a list in another file.
How to comparing two bacterial genomes and find the mutation, rearrangement etc.
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Recent Replies
Comment: differential gene expression analysis when not all samples have an untreated cou by nhaus ▴ 300
Thank you very much for your answer, that was very helpful! > Impossible to say. It depends on your data, particularly on how the donors …
Comment: QC exclusion of A/T or G/C alleles to avoid strand issues by bk11 ★ 2.3k
This could be because they are probably merging two or more datasets. If you are merging two or more datasets, it will be very important th…
Answer: Problem with Mirdeep2 and Randfold output by otieno43 ▴ 30
I sorted this out by first removing white space in the first line of the reference genome. Then indexed, the ran the mapper.pl script follo…
Comment: Questions about a bug when transferring cram file to bam file by GenoMax 141k
Just to be certain, you are saying that if OP runs `samtools view` without the explicit reference it will be automatically downloaded from …
Comment: Questions about a bug when transferring cram file to bam file by jkbonfield ★ 1.2k
That SQ M5 is chr1 in my copy of GRCh38 (Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa). I'm assuming your hg38.fa is not the sa…
Comment: What happened to Tombo Re-squiggle by Ram 43k
Please do not add answers unless you're answering the top level question. Instead, use `Add Comment` or `Add Reply` as appropriate. I've mo…
Comment: What happened to Tombo Re-squiggle by Joseph • 0
Hi, Does anybody has the answer to this? I also want to resquiggle my data with Remora but do not quite get which is the appropriate com…
Comment: How To Identify The 16S Rrna Gene Sequence In A Genome by colindaven 6.3k
It's also worth mentioning `Barrnap` is in the bacterial annotation system **Prokka**. `Prokka` can be installed on Debian systems with `…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa by Elisabeth Gasteiger ★ 2.4k
See also https://www.uniprot.org/help/negative_datasets
Comment: Sheep reference genome remapping coordinates by valentinatsar • 0
Thank you for your response As I can understand this tool takes sequence input files right? I have genome-wide genotypes instead of sequen…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa by me ▴ 750
Ok I made this into an answer. Could you please accept it as such.
Answer: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa by me ▴ 750
You can't. The data does not exist. UniProt only annotates where a lysine is know to be acetylated. There is no way that UniProt can know w…
Comment: How to compare the quality of assemblies by GenoMax 141k
Are there any short read datasets available in SRA? Can you try and see how many left over reads remain after you align to both of your ass…
Comment: Korean human genome reference file by GenoMax 141k
From NCBI: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_001712695.1/ Use the `Download` button or `curl/datasets`.
Comment: SLURM submission problem: Indexing the Reference Genome is not done in STAR by GenoMax 141k
> But it keeps giving error Please tell us what the error is.
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