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753 results • Page 2 of 16
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3
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9
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947
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How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 29 days ago by ★ 2.4k • written 4 weeks 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
0
votes
8
replies
464
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 28 days ago by 14k • written 9 months ago by ▴ 80
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
532
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
553
views
Downsampling fastq file
downsample fastq
17 days ago by marco.barr ▴ 130
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
8
votes
8
replies
761
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 23 days ago by 14k • written 24 days ago by ▴ 10
2
votes
8
replies
383
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
1
vote
8
replies
425
views
Overlapping Ranges within Granges object
Genomicranges IRanges GRanges
updated 4 hours ago by 35k • written 4 days ago by ▴ 60
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
0
votes
8
replies
460
views
Different output for read length
samtools BAM
8 days ago by marco.barr ▴ 130
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
1
vote
7
replies
505
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
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
3
votes
7
replies
417
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
2
votes
7
replies
961
views
Removing duplicates
duplicates ONT minimap2
updated 29 days ago by ▴ 580 • written 4 weeks ago by • 0
1
vote
7
replies
618
views
ScRNA data question
scRNA Vlnplot Samples
updated 18 days ago by ★ 2.5k • written 22 days ago by ▴ 10
0
votes
7
replies
445
views
RNAseq one control two conditions, shared and exclusive genes
conditions RNAseq multiple Rstudio
updated 5 days ago by ▴ 20 • written 18 days ago by • 0
6
votes
7
replies
391
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
1
vote
7
replies
541
views
Question regarding WGCNA
WGCNA Network-construction
8 days ago by deepak • 0
0
votes
7
replies
647
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
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
4
votes
7
replies
452
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA R VARIANCE
updated 20 hours ago by ▴ 130 • written 2 days ago by ▴ 20
4
votes
7
replies
609
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
5
votes
7
replies
496
views
RNA seq analysis
DESeq RNA-seq
3 days ago by Jacek ▴ 20
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
1
vote
7
replies
615
views
gvcf joint calling
WES GATK VCF gVCF
20 days ago by zihanss • 0
0
votes
7
replies
4.3k
views
B allele frequency (BAF)
snp
updated 4 hours ago by ▴ 10 • written 3.7 years ago by ▴ 90
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
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
0
votes
6
replies
446
views
How to slice a gvcf file with tabix?
Tabix bed gvcf
24 days ago by Sd • 0
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
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
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
3
votes
6
replies
491
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
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
0
votes
6
replies
2.1k
views
Copy number Variation analysis using conumee
R software error sequencing genome
updated 8 days ago by 142k • written 3.2 years ago by ▴ 10
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
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
1
vote
6
replies
408
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
5
votes
6
replies
603
views
Programmatically retrieving positions of protein active site residues
Uniprot PDB Proteins
updated 17 days ago by ▴ 760 • written 18 days ago by ▴ 40
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
7
votes
6
replies
599
views
Filtering sam or bam file with maximum matching region
crisper-edited alignment match
26 days ago by analyst ▴ 50
753 results • Page 2 of 16
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Recent Replies
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…
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 -…
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