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758 results • Page 2 of 16
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2
votes
9
replies
938
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TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 24 days ago by 4.2k • written 7 months 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 18 days ago by 43k • written 9 months ago by • 0
0
votes
8
replies
461
views
Error in cnetplot enrichplot package
R
updated 25 days ago by 43k • written 25 days ago by • 0
3
votes
8
replies
1.4k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq Cellranger STARsolo 10X
updated 27 days ago by 14k • written 9 months ago by ▴ 80
4
votes
8
replies
766
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs BED eqtl bedtools
updated 20 days ago by 35k • written 21 days ago by ▴ 10
1
vote
8
replies
950
views
Adding CB tag to bam file
samtools bam
updated 22 days ago by 161k • written 29 days ago by • 0
3
votes
8
replies
686
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
0
votes
8
replies
531
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
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
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
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
2
votes
8
replies
379
views
joint callset and vcf sorting, unknown TAG issue
sort bcftools GLNexus merge VCF
updated 5 days ago by 161k • written 5 days ago by ▴ 100
3
votes
8
replies
602
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
11 days ago by Qroid ▴ 40
0
votes
8
replies
455
views
Different output for read length
samtools BAM
8 days ago by marco.barr ▴ 130
8
votes
8
replies
755
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 22 days ago by 14k • written 23 days ago by ▴ 10
1
vote
8
replies
550
views
Downsampling fastq file
downsample fastq
17 days ago by marco.barr ▴ 130
2
votes
7
replies
955
views
Removing duplicates
duplicates ONT minimap2
updated 29 days ago by ▴ 580 • written 4 weeks ago by • 0
3
votes
7
replies
411
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
4
votes
7
replies
417
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
4 days ago by Chen • 0
6
votes
7
replies
387
views
Longest transcript variant per gene
transcript longest variant orthofinder
5 days ago by sansan_96 ▴ 90
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
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
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
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
0
votes
7
replies
441
views
RNAseq one control two conditions, shared and exclusive genes
conditions RNAseq multiple Rstudio
updated 4 days ago by ▴ 20 • written 18 days ago by • 0
0
votes
7
replies
642
views
Post-imputation plot
michigan-imputation-server quality-control
updated 15 days ago by 3.9k • written 18 days ago by ▴ 10
1
vote
7
replies
541
views
Question regarding WGCNA
WGCNA Network-construction
8 days ago by deepak • 0
1
vote
7
replies
614
views
gvcf joint calling
WES GATK VCF gVCF
19 days ago by zihanss • 0
2
votes
7
replies
5.3k
views
6 follow
Memory usage of picard Samsort
Picard SortSam
updated 28 days ago by 82k • written 7.2 years ago by ▴ 80
1
vote
7
replies
503
views
Downsampling long-read BAM files
nanopore BAM QC ONT downsampling
14 days ago by eebloom ▴ 80
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 6 days ago by • 0 • written 5.7 years ago by ▴ 20
1
vote
7
replies
613
views
ScRNA data question
scRNA Vlnplot Samples
updated 18 days ago by ★ 2.5k • written 22 days ago by ▴ 10
5
votes
7
replies
490
views
RNA seq analysis
DESeq RNA-seq
2 days ago by Jacek ▴ 20
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
440
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA R VARIANCE
updated 12 hours ago by ▴ 130 • written 2 days ago by ▴ 20
4
votes
7
replies
607
views
To get p-values for the TPM
P-value TPM RSEM
updated 22 days ago by ★ 6.0k • written 23 days ago by • 0
1
vote
7
replies
389
views
Overlapping Ranges within Granges object
Genomicranges IRanges GRanges
2 days ago by ntsopoul ▴ 60
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq RNA-Seq exon
updated 11 days ago by ▴ 30 • written 6.7 years ago by ★ 1.2k
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome sequencing singleton SNP filter
updated 17 days ago by ▴ 20 • written 9.7 years ago by ▴ 40
5
votes
6
replies
602
views
Programmatically retrieving positions of protein active site residues
Uniprot PDB Proteins
updated 17 days ago by ▴ 760 • written 18 days ago by ▴ 40
0
votes
6
replies
481
views
Differential Expression Analysis using DESeq2 in R
deseq2 R
updated 14 days ago by 14k • written 14 days ago by • 0
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient molecule at bam DNA RG ends clipping damage
updated 9 days ago by ▴ 10 • written 2.5 years ago by • 0
10
votes
6
replies
14k
views
7 follow
How To Identify The 16S Rrna Gene Sequence In A Genome
updated 29 days ago by 6.4k • written 10.9 years ago by ▴ 10
7
votes
6
replies
598
views
Filtering sam or bam file with maximum matching region
crisper-edited alignment match
26 days ago by analyst ▴ 50
2
votes
6
replies
386
views
BWA alignment
Samtools bam
updated 2 days ago by ▴ 260 • written 4 days ago by • 0
1
vote
6
replies
403
views
Do I need to go back and filter my long-reads?
alignment nanopore filtering QC ONT
updated 14 days ago by 142k • written 4 weeks ago by ▴ 80
2
votes
6
replies
3.8k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell RNAseq DE Analysis Treatment Control
updated 22 days ago by 82k • written 3.9 years ago by ▴ 280
3
votes
6
replies
489
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 5 days ago by ▴ 20 • written 12 days ago by • 0
0
votes
6
replies
211
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
3 hours ago by hannes.bongartz • 0
10
votes
6
replies
10k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly rna-seq alignment
updated 21 days ago by ★ 5.1k • written 6.0 years ago by ▴ 520
758 results • Page 2 of 16
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Recent Replies
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…
Answer: Trimming tool by GenoMax 142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by bk11 ★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
Comment: Reconstruction of locus, order contigs by dthorbur ★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
Comment: how to treat the replicates while performing WGCNA by andres.firrincieli 3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
Comment: How to systematically check if a bam file is truncated by alanh ▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
Comment: How to handle duplicated genes in TCGA data? by Zhenyu Zhang ★ 1.2k
Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by Ram 43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
Comment: Reconstruction of locus, order contigs by BATMAN • 0
I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
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