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503 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 21 hours 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
8
votes
10
replies
638
views
bash script
whole-genome-sequencing
updated 2 days ago by 43k • written 9 days ago by ▴ 30
6
votes
10
replies
1.6k
views
Integration of Microarray datasets with different platforms and biological groups
limma microarray DEA batch-effect
updated 8 hours ago by 43k • written 4.7 years ago by ▴ 60
5
votes
2
replies
1.7k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq batch batch-effect sequencing
updated 1 day ago by 43k • written 2.9 years ago by ▴ 60
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq bulk-RNASeq RNA-Seq single-cell
updated 7 days ago by • 0 • written 3.8 years ago by ★ 1.8k
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
5
votes
6
replies
378
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
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
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
4
votes
13
replies
740
views
RNAseq of primary tumor and metastases in two different organ
metastases RNA-seq DEG R
updated 23 hours ago by ★ 1.7k • written 6 days ago by • 0
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 22 days ago by 43k • written 5.5 years ago by ▴ 110
4
votes
4
replies
344
views
Average expression of a sample in single-cell data
single-cell rna-seq
15 days ago by newuser2024 • 0
4
votes
6
replies
822
views
bwa mem hangs after a few thousand reads
bwa alignment variant-calling bwa-mem
updated 15 days ago by 43k • written 4 months ago by ▴ 30
4
votes
9
replies
540
views
variant calling
variant-calling
updated 14 days ago by 43k • written 15 days ago by • 0
4
votes
7
replies
516
views
DESeq2 Multifactor Design
RNA-seq DESeq2
updated 4 days ago by 43k • written 5 days ago by ▴ 20
4
votes
7
replies
538
views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
JBrowse JBrowse2
updated 15 days ago by ★ 3.8k • written 19 days ago by ▴ 140
3
votes
4
replies
332
views
Single cell analysis with "meta".tsv.gz file
Single-cell
15 days ago by Estevão • 0
3
votes
3
replies
302
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio volcano-plot
18 days ago by Pumla • 0
3
votes
1
reply
253
views
how to change the gene header names in a fasta file?
fasta bioawk awk seqkit
updated 5 days ago by 43k • written 6 days ago by • 0
3
votes
12
replies
472
views
struggle to get fasta files from ucsc goldenPath
ucsc getfasta fasta
15 days ago by Lila M ★ 1.2k
3
votes
2
replies
208
views
Trying to write bwa mem -> samtools view -> samtools sort loop
bwa samtools mapping genome
updated 13 days ago by 161k • written 13 days ago by • 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
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq batch-effect DESeq2
updated 8 hours ago by 43k • written 4.4 years ago by ▴ 10
3
votes
2
replies
230
views
Gene reads all zero for each sample
R salmon DE DESeq2
20 days ago by DYLAN NICO • 0
3
votes
5
replies
389
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
updated 14 days ago by 141k • written 15 days ago by ▴ 190
3
votes
2
replies
294
views
Seeking Guidance on How to Annotate Unusual Cell Populations in Single-Cell Data
Transcriptomics Single-Cell
updated 12 days ago by 43k • written 6 weeks 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
1
reply
230
views
VEP annotation --per_gene allele choice
VEP
updated 5 days ago by 43k • written 5 days ago by ▴ 10
2
votes
6
replies
505
views
Need help understanding core SNPs
SNPs snippy
23 days ago by ujichu • 0
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 8 days ago by 43k • written 4.8 years ago by • 0
2
votes
0
replies
1.8k
views
ComBat-seq adjustment of batch effects
RNA-Seq ComBat-seq SVA edgeR batch-effect
updated 21 hours ago by 43k • written 3.4 years ago by ▴ 50
2
votes
6
replies
372
views
create a gene count matrix csv file from seurat object
Seurat sparseMatrix
9 days ago by jkim ▴ 170
2
votes
3
replies
922
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 2 days ago by 43k • written 4.1 years ago by ▴ 790
2
votes
2
replies
263
views
DepMap: siRNA and CRSIPR discrepancy
DepMap
updated 6 days ago by 81k • written 6 days ago by ★ 9.4k
2
votes
1
reply
232
views
Disease Prevalence Database/Disease Incidence Database
prevalence
updated 27 days ago by 43k • written 27 days ago by ★ 9.4k
2
votes
3
replies
250
views
Reference mouse phased vcf
mm10 vcf phasing Beagle
23 days ago by machoo • 0
2
votes
2
replies
239
views
Removing adapters in all the RNAseq samples regardless if they have or not, is it correct?
fastqc trimming adapters cutadapt RNAseq
updated 14 days ago by ★ 5.8k • written 14 days ago by ▴ 20
2
votes
2
replies
258
views
A pipeline for prediction and annotation of obelisks
rna-seq
updated 21 days ago by 161k • written 22 days ago by ▴ 110
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
15 days ago by b.contreras.moreira ▴ 150
2
votes
5
replies
1.5k
views
Adding functional annotation and meta-data of MAKER/BRAKER GFF
metadata functional-annotation BRAKER MAKER
updated 16 days ago by ▴ 40 • written 15 months ago by ▴ 60
2
votes
5
replies
656
views
samtools mpileup taking too long
Bam samtools sam alignment
updated 12 days ago by 43k • written 5 weeks 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 12 days ago by 43k • written 2.9 years ago by • 0
2
votes
4
replies
266
views
Addmetadata to seurat obj
seurat
7 days ago by synat.keam ▴ 100
2
votes
2
replies
216
views
How to establish haplotype-specific gene expression levels
RNA-seq Haplotype
7 days ago by javanokendo ▴ 60
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 20 hours ago by 43k • written 7.4 years ago by • 0
2
votes
2
replies
320
views
Seeking help with Tcga Target Gtex Expected Count Data
R TCGA gTEX
25 days ago by bioinfo_enthusiast • 0
2
votes
4
replies
366
views
Per Base Sequence Content - continuous raise of G%
fastqc
updated 7 days ago by 141k • written 8 days ago by • 0
2
votes
3
replies
241
views
P-value Threshold Consideration in Multi-Sample RNA-Seq Experiment
statistics RNA-Seq p-value
updated 15 days ago by 43k • written 15 days ago by • 0
2
votes
12
replies
683
views
Nanopore data filtering using fastp
fastp nanopore
20 days ago by emilydolivo97 ▴ 10
503 results • Page 1 of 11
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High fold change values
C: Bcftools Mpileup Removes Marked Duplicates?
Prediction tools summary - zero values
A: Error with Formatdb of legacy blast?
Error with Formatdb of legacy blast?
Answer: How to convert SAM/BAM file to GTF/GFF file?
A: Ribo-seq vs RNA-seq read count
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Recent Replies
Comment: Removing duplicates by joe ▴ 490
I *could* imagine an ONT scenario where you'd want to remove duplicates (amplicon-seq, etc) but likely for variant calling there is no need…
Comment: Removing duplicates by samuel.a.odonnell ▴ 510
As above, you do not need to worry about duplicates for ONT data Also have you looked at using other tools for variant calling more suited…
Answer: Pediococcus acidilactici sequence analysis by geneontologyhelp ▴ 340
If you're looking for the GO annotations for *Pediococcus acidilactici*, these are available. Using the instructions under [*2. All other…
Answer: What is the normalization status of metabric data? by etiennedanis ▴ 10
I just found an answer to this question here: [https://groups.google.com/g/cbioportal/c/hm_i4jbG1uc/m/h9rNYOvpAAAJ][1] [1]: https://gro…
Comment: Removing duplicates by joe ▴ 490
With ONT you will only have PCR duplicates. 'Read' (you mean optical?) duplicates are an artifact of cluster-based sequencing (ie Illumina)…
Comment: assembly using CCS, CLR, CCS_CLR sequences together? by GenoMax 141k
PacBio has some recommendations on software for genome assemblies on this page (which you may have seen but just in case): https://www.pacb…
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions by swbarnes2 14k
I would not put totally different tissues in the same DESeq object. I don't think that's going to do good things for normalization or disp…
Comment: Removing duplicates by quentinperriere • 0
pcr duplicates or/and read duplicates should I use this command to remove them ? or we don't talk about duplicates when dealing with ONT ??…
Comment: How to reduce the variation of CIBERSORTx results? by LChart 3.9k
If you didn't change the input signature matrix, the input RNA matrix, or the input parameters - what did you change? Is the statement that…
Answer: Inconsistency in SNP detection pipelines for multi-sample analysis by LChart 3.9k
> To replicate GVCF behavior and avoid issues with 0/0 genotypes appearing as missing, I don't use the -v option I'm not sure what you m…
Comment: Supergnova stuck in tutorial by GenoMax 141k
Your best option may be to email the author (and/or the senior author from the paper). Let them know that the FTP links mentioned on GitHub…
Comment: DEG analysis of RNA-seq data across multiple tissues and two conditions by BioinfGuru ★ 1.7k
Thanks @lchart, I accept that, I'll wait to see if there's any more who want to input and then accept the answer
Comment: Per base sequence content failed miserably by GenoMax 141k
What kind of data is this? Plain genomic/amplicons? How you proceed will largely depend on the context. Can you also post the original fast…
Comment: Removing duplicates by samuel.a.odonnell ▴ 510
I guess the enlightening question is: duplicates of what?
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions by LChart 3.9k
I don't think this approach will give you what you want. Combining multiple tissues in the way you are suggesting will result in a positive…
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