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740 results • Page 2 of 15
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2
votes
8
replies
385
views
joint callset and vcf sorting, unknown TAG issue
sort bcftools GLNexus merge VCF
updated 6 days ago by 161k • written 6 days ago by ▴ 100
1
vote
8
replies
431
views
Overlapping Ranges within Granges object
Genomicranges IRanges GRanges
updated 10 hours ago by 35k • written 4 days ago by ▴ 60
0
votes
8
replies
466
views
Error in cnetplot enrichplot package
R
updated 25 days ago by 43k • written 25 days ago by • 0
0
votes
8
replies
534
views
What does it mean single base resolution in sequencing?
SNP sequencing
updated 17 days ago by 4.2k • written 19 days ago by ▴ 10
3
votes
8
replies
5.0k
views
An idea to identify batch effects
microarray batch-effect
updated 29 days ago by 43k • written 9.7 years ago by • 0
1
vote
8
replies
555
views
Downsampling fastq file
downsample fastq
17 days ago by marco.barr ▴ 130
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 29 days ago by 43k • written 4.6 years ago by ▴ 180
1
vote
8
replies
952
views
Adding CB tag to bam file
samtools bam
updated 23 days ago by 161k • written 29 days ago by • 0
4
votes
8
replies
772
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs BED eqtl bedtools
updated 21 days ago by 35k • written 22 days ago by ▴ 10
3
votes
8
replies
690
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 11 days ago by ▴ 410 • written 15 days ago by ▴ 100
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk genomicsdbimport
updated 15 days ago by • 0 • written 5.1 years ago by 11k
0
votes
8
replies
462
views
Different output for read length
samtools BAM
8 days ago by marco.barr ▴ 130
3
votes
8
replies
604
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
11 days ago by Qroid ▴ 40
8
votes
8
replies
764
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 23 days ago by 14k • written 24 days ago by ▴ 10
4
votes
7
replies
463
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA R VARIANCE
updated 1 day ago by ▴ 130 • written 2 days ago by ▴ 20
2
votes
7
replies
961
views
Removing duplicates
duplicates ONT minimap2
updated 29 days ago by ▴ 580 • written 4 weeks ago by • 0
7
votes
7
replies
6.0k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq SNP
updated 22 days ago by ▴ 860 • written 6.2 years ago by ▴ 10
3
votes
7
replies
419
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc cutadapt illumina tile paired-end
18 days ago by salias • 0
1
vote
7
replies
508
views
Downsampling long-read BAM files
nanopore BAM QC ONT downsampling
15 days ago by eebloom ▴ 80
0
votes
7
replies
446
views
RNAseq one control two conditions, shared and exclusive genes
conditions RNAseq multiple Rstudio
updated 5 days ago by ▴ 20 • written 19 days ago by • 0
0
votes
7
replies
649
views
Post-imputation plot
michigan-imputation-server quality-control
updated 15 days ago by 3.9k • written 18 days ago by ▴ 10
2
votes
7
replies
5.3k
views
6 follow
Memory usage of picard Samsort
Picard SortSam
updated 29 days ago by 82k • written 7.2 years ago by ▴ 80
1
vote
7
replies
542
views
Question regarding WGCNA
WGCNA Network-construction
9 days ago by deepak • 0
1
vote
7
replies
618
views
ScRNA data question
scRNA Vlnplot Samples
updated 18 days ago by ★ 2.5k • written 23 days ago by ▴ 10
6
votes
7
replies
393
views
Longest transcript variant per gene
transcript longest variant orthofinder
5 days ago by sansan_96 ▴ 90
5
votes
7
replies
498
views
RNA seq analysis
DESeq RNA-seq
3 days ago by Jacek ▴ 20
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat RNA-Seq Limma DESeq2 batch-effect
updated 29 days ago by 43k • written 5.0 years ago by ▴ 140
4
votes
7
replies
611
views
To get p-values for the TPM
P-value TPM RSEM
updated 23 days ago by ★ 6.0k • written 24 days ago by • 0
2
votes
7
replies
1.4k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq Salmon Isoseq
updated 19 days ago by ★ 7.2k • written 8 months ago by ▴ 10
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 7 days ago by • 0 • written 5.7 years ago by ▴ 20
1
vote
7
replies
616
views
gvcf joint calling
WES GATK VCF gVCF
20 days ago by zihanss • 0
4
votes
7
replies
424
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
4 days ago by Chen • 0
0
votes
7
replies
1.9k
views
Batch effect correction in RNASeq data and plot Dendrograms cluster
clustering dendrogram RNA-Seq batch-effect
updated 29 days ago by 43k • written 4.1 years ago by ▴ 500
4
votes
7
replies
635
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
18 days ago by e.r.zakiev ▴ 210
0
votes
7
replies
4.3k
views
B allele frequency (BAF)
snp
updated 10 hours ago by ▴ 10 • written 3.7 years ago by ▴ 90
6
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon human bed v7 agilent all sureselect
updated 12 days ago by ▴ 10 • written 2.0 years ago by • 0
0
votes
6
replies
269
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
16 hours ago by hannes.bongartz • 0
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN DNA methylation Funnorm
updated 21 days ago by 43k • written 2.4 years ago by ▴ 10
3
votes
6
replies
493
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 5 days ago by ▴ 20 • written 13 days ago by • 0
0
votes
6
replies
450
views
How to slice a gvcf file with tabix?
Tabix bed gvcf
24 days ago by Sd • 0
2
votes
6
replies
1.9k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML ncbi entrez-direct
updated 2 days ago by 43k • written 3.9 years ago by • 0
10
votes
6
replies
10k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly rna-seq alignment
updated 22 days ago by ★ 5.1k • written 6.0 years ago by ▴ 520
1
vote
6
replies
729
views
anRichment is missing
WGCNA anRichment
updated 11 days ago by 142k • written 6 months ago by ▴ 180
4
votes
6
replies
808
views
7 follow
Heatmap and rna-seq
RNA-Seq Heatmap
updated 21 days ago by ★ 6.0k • written 25 days ago by ▴ 10
2
votes
6
replies
5.3k
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 29 days ago by 43k • written 3.8 years ago by • 0
0
votes
6
replies
490
views
Differential Expression Analysis using DESeq2 in R
deseq2 R
updated 14 days ago by 14k • written 15 days ago by • 0
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq RNA-Seq exon
updated 12 days ago by ▴ 30 • written 6.7 years ago by ★ 1.2k
7
votes
6
replies
600
views
Filtering sam or bam file with maximum matching region
crisper-edited alignment match
26 days ago by analyst ▴ 50
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma gwas
updated 19 days ago by • 0 • written 5.0 years ago by ▴ 90
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome sequencing singleton SNP filter
updated 18 days ago by ▴ 20 • written 9.7 years ago by ▴ 40
740 results • Page 2 of 15
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Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
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Comment: ChatGPT optimized for bioinformatics questions
C: How can I perform Differential expression analysis with just one control and one
C: How can I perform Differential expression analysis with just one control and one
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Recent Replies
Comment: calculating genomic coverage/ base overlap in R by 1769mkc ★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks by ATpoint 82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner by Joe 21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression? by Gordon Smyth ★ 7.2k
See the exploration of isoform precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Table 1 o…
Comment: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA by mavy ▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object by Alex Reynolds 35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF) by aidangcruickshank ▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data? by Ngrin • 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2 by swbarnes2 14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot by LauferVA 4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot by bk11 ★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool by ntsopoul ▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
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