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1,000 results • Page 5 of 20
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3
votes
7
replies
1.5k
views
Find 3'UTRs for species
Assembly alignment
updated 11 months ago by 43k • written 4.7 years ago by ▴ 110
0
votes
7
replies
940
views
SNPeff problem
snpEff
updated 10 months ago by 43k • written 10 months ago by • 0
2
votes
7
replies
713
views
Does removal of contaminants in RNAseq data have an impact on downstream analyses?
RNA-seq contamination
updated 9 weeks ago by ▴ 410 • written 9 weeks ago by ▴ 20
2
votes
7
replies
1.3k
views
Weirdness in annotation (missing allele frequencies)
allele-frequency gnomad annovar
updated 7 months ago by 43k • written 7 months ago by • 0
4
votes
7
replies
2.2k
views
About normalization of the datasets from Harmonized TCGA data
protein transcript normalisation
updated 3 months ago by 43k • written 22 months ago by ▴ 10
4
votes
7
replies
646
views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
JBrowse JBrowse2
updated 6 weeks ago by ★ 3.8k • written 7 weeks ago by ▴ 140
4
votes
7
replies
795
views
Alternative for grep in a for loop
linux
updated 7 months ago by 43k • written 7 months ago by ▴ 20
3
votes
7
replies
6.3k
views
running trimmomatic inside Trinity
Assembly Trinity RNA-seq trimmomatic
updated 10 months ago by 43k • written 8.1 years ago by ▴ 50
0
votes
7
replies
1.9k
views
monocle single cell differential expression: error message for HSMM <- estimateDispersions(HSMM) command
single-cell monocle
updated 10 months ago by 3.9k • written 2.4 years ago by ▴ 40
0
votes
7
replies
587
views
Iterate through Seurat object to add patient information
R Seurat
updated 3 months ago by 43k • written 3 months ago by ▴ 100
4
votes
7
replies
634
views
DESeq2 Multifactor Design
RNA-seq DESeq2
updated 4 weeks ago by 43k • written 5 weeks ago by ▴ 20
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression RNA-Seq GTex DESeq2
updated 5 weeks ago by 43k • written 6.5 years ago by ▴ 10
7
votes
7
replies
5.0k
views
RNA-Seq time series analysis using a DESeq2 spline approach yields far too many significant genes
splines DESeq2 time-series RNA-Seq
updated 11 months ago by 43k • written 5.3 years ago by ▴ 80
0
votes
7
replies
2.9k
views
qPCR: Huge variation in fold change of genes between biological replicates
qpcr fold-change
updated 8 months ago by 43k • written 5.9 years ago by ▴ 80
2
votes
7
replies
1.4k
views
VG mapping paired-end reads: error [xg]: multiple hits for XXX
variation-graph reads pangenome vg paired-end
8 months ago by nkls063408 • 0
3
votes
7
replies
2.6k
views
6 follow
Online BLAST search using R
BLAST R
updated 3 months ago by ▴ 140 • written 2.8 years ago by ▴ 20
0
votes
7
replies
552
views
SNP calling with many samples using bcftools
bcftools SNP multithreading
6 months ago by George ▴ 10
3
votes
7
replies
6.4k
views
Human reference files in HG38 GATK resource bundle
VCF
updated 11 months ago by ★ 4.3k • written 6.3 years ago by ▴ 980
3
votes
7
replies
3.3k
views
vcf filter for FORMAT argument (DP/GQ/GQX > 30) multiple (380) vcf file
vcffilter vcftools sequencing
updated 10 months ago by 43k • written 4.2 years ago by ▴ 10
1
vote
7
replies
834
views
What could be the rage for Average Coverage after Assembly
viral-genome spades coverage de-novo-assembly
updated 10 months ago by 43k • written 10 months ago by ▴ 70
1
vote
7
replies
884
views
Ribosomal cluster
seurat single-cell
7 months ago by Chris ▴ 280
4
votes
7
replies
845
views
SNP IDs
SNP
6 months ago by kl ▴ 10
10
votes
7
replies
3.7k
views
What is Pathway Analysis?
database analysis ontology pathway
updated 11 months ago by 43k • written 8.1 years ago by ▴ 330
3
votes
7
replies
544
views
How does kallisto handle multi mapped reads?
kallisto
updated 12 weeks ago by ★ 6.0k • written 12 weeks ago by ▴ 150
0
votes
7
replies
667
views
Using Primer3 with python to genotype a SNP at a particular position
primer3 python position primer
updated 6 months ago by 161k • written 6 months ago by • 0
0
votes
7
replies
1.0k
views
All question mark quality scores on several studies
quality-score shotgun illumina
updated 11 months ago by 43k • written 11 months ago by ▴ 10
3
votes
7
replies
1.4k
views
VG Giraffe multi-mapped reads and definition for MAPQ score
vg
9 months ago by Hendricks27 • 0
1
vote
7
replies
4.1k
views
Adjust width of annotations in pheatmap
R heatmap
updated 7 months ago by 88k • written 5.5 years ago by ▴ 30
8
votes
7
replies
1.1k
views
Why does Ensembl VEP provide HGVSg for some variants and not others?
vcf VEP
11 months ago by Jeremy Leipzig 22k
0
votes
7
replies
960
views
For loop RNA Sequencing alignment
RNA STAR
updated 11 months ago by 43k • written 19 months ago by • 0
0
votes
7
replies
2.0k
views
CIBERSORTx error: 'x' must be an array of at least two dimensions
matrix CIBERSORTx signature
updated 6 months ago by • 0 • written 22 months ago by • 0
3
votes
7
replies
1.1k
views
IGV not showing bigwig track information
bigwig IGV ChIP-seq
updated 6 months ago by 82k • written 6 months ago by ▴ 10
0
votes
7
replies
6.1k
views
Pre-processing of RNA-Seq data for WGCNA
RNA-Seq WGCNA removeBatchEffect DESeq2
updated 4 weeks ago by 43k • written 7.7 years ago by ▴ 70
0
votes
7
replies
408
views
single nuclei sequencing questions
fastq single-nuclei-sequencing
updated 10 weeks ago by 43k • written 10 weeks ago by • 0
1
vote
7
replies
1.6k
views
cannot execute binary file: Exec format error
linux
updated 9 months ago by 54k • written 9 months ago by • 0
6
votes
7
replies
601
views
NF-Core ampliseq - Rscript markdown error
nf-core ampliseq
updated 4 months ago by 54k • written 4 months ago by • 0
0
votes
7
replies
2.2k
views
Command not found after pip install spliceai
software error
updated 7 months ago by • 0 • written 3.5 years ago by • 0
5
votes
7
replies
974
views
Are datasets for a unique cells, that downloded using sratoolkit?
RNA-Seq sequencing
updated 12 months ago by • 0 • written 4.4 years ago by ▴ 50
0
votes
7
replies
729
views
create an all against all fasta file
python fasta
updated 7 months ago by 43k • written 7 months ago by • 0
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect DESeq2 combat_seq
updated 5 weeks ago by 43k • written 3.7 years ago by ▴ 20
1
vote
7
replies
1.9k
views
for loop in a bash script
bash
updated 11 months ago by 43k • written 2.6 years ago by • 0
7
votes
7
replies
620
views
6 follow
PCA plot interpretation (single population)
PCA GWAS pruning
3 months ago by Shane ▴ 20
0
votes
7
replies
481
views
1000 Genome: Cause of duplicate variants with different genotypes
CrossMap 1000Genome 1000G
updated 3 months ago by ▴ 400 • written 3 months ago by ▴ 210
2
votes
7
replies
4.7k
views
SRA toolkit internet settings
sratoolkit fastq-dump sequencing RNA-Seq
updated 10 months ago by 43k • written 7.8 years ago by ▴ 90
5
votes
7
replies
495
views
RNA seq analysis
DESeq RNA-seq
2 days ago by Jacek ▴ 20
4
votes
7
replies
2.7k
views
low bootstrap value?
phylogeny genome alignment
updated 11 months ago by 43k • written 4.9 years ago by ▴ 120
0
votes
7
replies
738
views
error MarkerScanner.pl
amphora2
updated 5 months ago by 43k • written 5 months ago by • 0
0
votes
7
replies
1.0k
views
Issue with Merging BCF Files: Invalid INFO id Error
bcftools
updated 5 months ago by 43k • written 6 months ago by ▴ 10
5
votes
7
replies
986
views
Salmon index not progressing
salmon
updated 7 months ago by 54k • written 7 months ago by ▴ 160
5
votes
7
replies
3.2k
views
8 follow
bwa mem -T (alignment score) not doing anything
SNP genome sequence
updated 7 months ago by 100k • written 5.9 years ago by ▴ 10
1,000 results • Page 5 of 20
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Recent Replies
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 -…
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…
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