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896 results • Page 2 of 18
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4
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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
11
votes
9
replies
7.0k
views
How to choose method to integrate different patient sample together in Seurat
Seurat scRNA batch-effect harmony
updated 28 days ago by 43k • written 4.2 years ago by ▴ 80
2
votes
9
replies
936
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 21 days ago by 4.2k • written 7 months ago by • 0
1
vote
9
replies
1.3k
views
Supergnova stuck in tutorial
Genetic Correlations Python Supergnova Conda
updated 27 days ago by • 0 • written 20 months ago by ▴ 10
2
votes
9
replies
678
views
Filtering Multi-sample VCF file for all except one Genotype
variant SNP VCF
updated 12 hours ago by 161k • written 8 days 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 28 days ago by 43k • written 4.0 years ago by ▴ 20
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 7 days ago by • 0 • written 5.8 years ago by ▴ 30
1
vote
9
replies
4.7k
views
Help with multiple batch effects
sva combat batch-effect
updated 28 days ago by 43k • written 5.9 years ago by ▴ 30
0
votes
9
replies
567
views
Applying the metacell2 algorithm using python
python single-cell scanpy metacell2
updated 5 hours ago by ★ 2.0k • written 9 days ago by ▴ 140
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 12 days ago by • 0 • written 2.2 years ago by • 0
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference 38build impute imputation
16 days ago by anna ▴ 20
3
votes
9
replies
937
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 27 days ago by ★ 2.4k • written 27 days ago by • 0
3
votes
9
replies
607
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 21 days ago by 100k • written 23 days ago by • 0
0
votes
9
replies
2.6k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome base-calling fastq nanopore
updated 16 days ago by 43k • written 8 months ago by • 0
6
votes
8
replies
659
views
BRAKER3 genome annotation
annotation BRAKER3 genome
updated 28 days ago by 14k • written 4 weeks ago by ▴ 40
1
vote
8
replies
940
views
Adding CB tag to bam file
samtools bam
updated 20 days ago by 161k • written 26 days ago by • 0
8
votes
8
replies
745
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 20 days ago by 14k • written 21 days ago by ▴ 10
2
votes
8
replies
348
views
joint callset and vcf sorting, unknown TAG issue
sort bcftools GLNexus merge VCF
updated 3 days ago by 161k • written 3 days ago by ▴ 100
3
votes
8
replies
568
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
9 days ago by Qroid ▴ 40
4
votes
8
replies
759
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs BED eqtl bedtools
updated 18 days ago by 35k • written 19 days ago by ▴ 10
1
vote
8
replies
531
views
Downsampling fastq file
downsample fastq
15 days ago by marco.barr ▴ 110
1
vote
8
replies
3.5k
views
Best way to address different batches of RNA-seq
sequence RNA-Seq RPKM Fold-Change batch-effect
updated 28 days ago by 43k • written 7.1 years ago by ▴ 20
3
votes
8
replies
4.2k
views
Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
fpkm scRNA-seq RNA-Seq tpm batch-effect
updated 27 days ago by 43k • written 4.6 years ago by ▴ 180
3
votes
8
replies
1.4k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq Cellranger STARsolo 10X
updated 25 days ago by 14k • written 9 months ago by ▴ 80
3
votes
8
replies
5.0k
views
An idea to identify batch effects
microarray batch-effect
updated 27 days ago by 43k • written 9.7 years ago by • 0
0
votes
8
replies
248
views
Duplicated reads (IDs) from nanopore sequencing
bam nanopore sequencing
updated 4 hours ago by 142k • written 13 hours ago by ▴ 20
0
votes
8
replies
453
views
Error in cnetplot enrichplot package
R
updated 22 days ago by 43k • written 23 days ago by • 0
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk genomicsdbimport
updated 13 days ago by • 0 • written 5.1 years ago by 11k
0
votes
8
replies
520
views
What does it mean single base resolution in sequencing?
SNP sequencing
updated 15 days ago by 4.2k • written 17 days ago by ▴ 10
3
votes
8
replies
675
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core 16S amplicon dada2 ampliseq
updated 9 days ago by ▴ 410 • written 13 days ago by ▴ 100
0
votes
8
replies
438
views
Different output for read length
samtools BAM
6 days ago by marco.barr ▴ 110
1
vote
7
replies
526
views
Question regarding WGCNA
WGCNA Network-construction
6 days ago by deepak • 0
3
votes
7
replies
1.0k
views
Can I use batch effect correction "by parts"?
ComBat RNA-Seq batch-effect
updated 28 days ago by 43k • written 4.4 years ago by ▴ 360
0
votes
7
replies
620
views
Post-imputation plot
michigan-imputation-server quality-control
updated 12 days ago by 3.9k • written 16 days ago by ▴ 10
1
vote
7
replies
603
views
gvcf joint calling
WES GATK VCF gVCF
17 days ago by zihanss • 0
2
votes
7
replies
1.4k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq Salmon Isoseq
updated 16 days ago by ★ 7.2k • written 8 months ago by ▴ 10
6
votes
7
replies
367
views
Longest transcript variant per gene
transcript longest variant orthofinder
3 days ago by sansan_96 ▴ 90
0
votes
7
replies
409
views
RNAseq one control two conditions, shared and exclusive genes
conditions RNAseq multiple Rstudio
updated 2 days ago by ▴ 20 • written 16 days ago by • 0
4
votes
7
replies
628
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
16 days ago by e.r.zakiev ▴ 210
1
vote
7
replies
606
views
ScRNA data question
scRNA Vlnplot Samples
updated 16 days ago by ★ 2.4k • written 20 days ago by ▴ 10
1
vote
7
replies
364
views
Overlapping Ranges within Granges object
Genomicranges IRanges GRanges
16 hours ago by ntsopoul ▴ 60
2
votes
7
replies
939
views
Removing duplicates
duplicates ONT minimap2
updated 26 days ago by ▴ 580 • written 28 days ago by • 0
3
votes
7
replies
553
views
Integration of transcriptomics and proteomics: difficult matching names
rna-seq tmt nomenclature proteomics
29 days ago by ntsopoul ▴ 60
4
votes
7
replies
389
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
1 day ago by Chen • 0
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 4 days ago by • 0 • written 5.7 years ago by ▴ 20
3
votes
7
replies
392
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc cutadapt illumina tile paired-end
16 days ago by salias • 0
2
votes
7
replies
5.3k
views
6 follow
Memory usage of picard Samsort
Picard SortSam
updated 26 days ago by 82k • written 7.2 years ago by ▴ 80
0
votes
7
replies
1.9k
views
Batch effect correction in RNASeq data and plot Dendrograms cluster
clustering dendrogram RNA-Seq batch-effect
updated 27 days ago by 43k • written 4.0 years ago by ▴ 500
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat RNA-Seq Limma DESeq2 batch-effect
updated 27 days ago by 43k • written 5.0 years ago by ▴ 140
7
votes
7
replies
6.0k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq SNP
updated 20 days ago by ▴ 860 • written 6.2 years ago by ▴ 10
896 results • Page 2 of 18
Recent Votes
Answer: featureCounts output summary assigned value higher than uniquely mapped reads fr
Answer: Doubt about the process of annotation, detection, identification and classificat
Answer: Filtering VCF files based on VAF giving incorrect results
Problems with breakdancer (sv caller) output.
Problems with breakdancer (sv caller) output.
Comment: Add stats to boxplot in R
Answer: Genotyping sites with N in reference genome
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Popular Question to Jean-Karim Heriche 27k
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Recent Replies
Comment: Filtering VCF files based on VAF giving incorrect results by Pierre Lindenbaum 161k
> Do you think my commands were correct? I'm not familiar enough with this bcftools syntax. but what if there is no AD, what if both…
Answer: How can you *consistently* download BioProject IDs from NCBI's BioSample databas by Ash • 0
I know this was asked several years ago, but finding this post helped me solve my own problem and in the process I solved this one too. …
Answer: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by swbarnes2 14k
Would Parkinson's be expected to have an effect on blood cells? Neurons, sure, but blood cells?
Comment: Doubt about the process of annotation, detection, identification and classificat by MarcosCosta • 0
Thank you very much, you've helped me a lot. Could you suggest a book or article that offers a complete explanation of these processes?
Comment: Filtering VCF files based on VAF giving incorrect results by Arton • 0
Thank you. I can't try a completely new tool but I will keep your command for future use. Do you think my commands were correct? For exampl…
Comment: Add stats to boxplot in R by Ghada • 0
Thanks. Thats work
Comment: Genotyping sites with N in reference genome by Zhenyu Zhang ★ 1.2k
Whether N -> A/T/G/C represents a variant is heavily dependent on the tool itself, and I know most tools don't. Since you don't see it in y…
Comment: calculating genomic coverage/ base overlap in R by marco.barr ▴ 110
The code seems correct at first glance... How did you generate the data in the Excel file? Have you checked the exon annotations? You could…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by GenoMax 142k
Did you remeber to unzip/untar the `nt` preformatted files that you downloaded?
Comment: Genotyping sites with N in reference genome by shpak.max ▴ 50
Just to clarify, I have set additional sites in the reference genome to 'N', which means (based on your statement) that these will not be g…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by Pierre Lindenbaum 161k
see https://www.biostars.org/p/9496674/ <!-- when i runed blastn(version 2.15) and nt database(latest version). I used aspera to download…
Answer: Genotyping sites with N in reference genome by Pierre Lindenbaum 161k
> Does UnifiedGenotyper skip/ignore sites where the reference genotype is N yes. The variant is in YOUR data, not in the reference where '…
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline? by yura.grabovska ▴ 70
Do you have samples that should in theory have a good degree over overlap in terms of cell types across the two sequencing types? I would …
Comment: Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file by asalimih ▴ 60
I found out that vep is only checking the GT field therefore assigning HOM to the Zygosity. Therefore the problem should be from deepvarian…
Comment: Add stats to boxplot in R by Lélé ▴ 10
To remove "Kruskall Wallis" you can try adding the argument label="p" or label = "p.signif" which displays the p-value or *** like this: …
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