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1,000 results • Page 5 of 20
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3
votes
4
replies
3.5k
views
any recommended tools for batch effect and normalization not written in R?
R RNA-Seq combat python batch-effect
updated 29 days ago by 43k • written 7.2 years ago by ▴ 310
3
votes
5
replies
553
views
How to assess the quality of the assembly of unmapped reads ?
Pangenome Iterative-assembly
3 months ago by Sony ▴ 10
3
votes
5
replies
3.2k
views
GO annotation for rice in an R package
annotation R
updated 3 months ago by • 0 • written 7.5 years ago by ▴ 10
3
votes
5
replies
1.2k
views
kraken2 bacteria database 250GB+
metagenomics 16s kraken2 kraken
updated 6 months ago by 142k • written 6 months ago by ▴ 10
3
votes
19
replies
1.6k
views
Systematic errors at the end and beginning of reads in NGS panels
NGS error panels sequencing
updated 10 months ago by 10k • written 10 months ago by ▴ 20
3
votes
9
replies
814
views
Understanding this analysis pipeline
reads
updated 10 months ago by 43k • written 10 months ago by • 0
3
votes
1
reply
562
views
chromosome location to gene name and aa change
variant-annotation
12 months ago by Zi • 0
3
votes
4
replies
827
views
Downstream analysis with DEseq2 normalization
DEseq2 integration
5 months ago by QX • 0
3
votes
3
replies
1.1k
views
Differentially Expressed Genes between two conditions (scRNA, single GEO dataset with multiple samples and no cell annotations)
scRNA-seq RNA-Seq Seurat
updated 7 months ago by ★ 2.5k • written 7 months ago by ▴ 10
3
votes
5
replies
1.6k
views
Uniprot API access to download .pdb files
PDB API Python Uniprot
11 months ago by BioGrad321 • 0
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression Salmon
updated 5 weeks ago by 43k • written 5.6 years ago by ▴ 100
3
votes
5
replies
699
views
Salmon loop on multiple samples
Salmon
updated 7 months ago by 43k • written 7 months ago by • 0
3
votes
5
replies
1.3k
views
Running purge_dups on a hybrid assembly (optical mapping + reads)
pacbio purge_dups Assembly bionano
updated 8 months ago by 6.4k • written 3.3 years ago by ▴ 300
3
votes
3
replies
614
views
How do mRNASeq, BulkRNASeq, and TotalRNASeq differ in terms of workflow?
RNA-Seq
updated 7 months ago by 43k • written 7 months ago by • 0
3
votes
1
reply
434
views
Best Tools and Practices for CNV Variant Calling in WES Data
CNV WES
updated 8 months ago by 161k • written 8 months ago by ▴ 20
3
votes
5
replies
706
views
ATAC-Seq and featureCounts
ATAC-Seq featureCounts
updated 4 months ago by 82k • written 4 months ago by ▴ 10
3
votes
3
replies
351
views
learning bioinformatics
course learning
updated 3 months ago by 43k • written 3 months ago by • 0
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
3
replies
551
views
Free/open source 23andme-like analysis
SNPs genomics NGS VCF
updated 27 days ago by 14k • written 29 days ago by ▴ 580
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
3
votes
6
replies
2.5k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq combat rna-seq sva batch-effect
updated 4 weeks ago by 43k • written 22 months ago by ▴ 20
3
votes
3
replies
517
views
Need Control Gene Count Files
R RNA-Seq TCGA
updated 6 months ago by ▴ 20 • written 6 months ago by ▴ 30
3
votes
5
replies
1.4k
views
AlphaMissense Plugin VEP
Plugin VEP Alphamissense
updated 7 months ago by 43k • written 7 months ago by ▴ 10
3
votes
6
replies
833
views
Annotating genome based on Sequence
genome annotation
updated 6 months ago by 4.6k • written 6 months ago by ▴ 30
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 9 days ago by • 0 • written 5.6 years ago by 8.5k
3
votes
14
replies
6.0k
views
remote command line BLAST job ends in CPU error and gives MBEDTLS version mismatch
blastn mbedtls blast linux blast+
updated 4 months ago by ▴ 40 • written 3.1 years 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
3
votes
4
replies
5.2k
views
What does this Warning in HTSeq-count means? (Warning: Mate pairing was ambiguous)
RNA-Seq
updated 9 months ago by ▴ 10 • written 8.7 years ago by ★ 1.4k
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
3
votes
7
replies
1.4k
views
VG Giraffe multi-mapped reads and definition for MAPQ score
vg
9 months ago by Hendricks27 • 0
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
3
votes
4
replies
4.4k
views
Atypical volcano plot RNA-seq
volcano-plot RNA-seq deseq2
updated 8 months ago by 43k • written 5.5 years ago by ▴ 20
3
votes
3
replies
881
views
from fasta to gtf format?
gtf DE fasta
updated 4 months ago by ▴ 210 • written 3.1 years ago by ▴ 260
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq batch-effect DESeq2
updated 4 weeks ago by 43k • written 4.5 years ago by ▴ 10
3
votes
6
replies
879
views
Read multiple vcf files into R
R vcf
6 months ago by sousapaulo16 ▴ 20
3
votes
5
replies
1.1k
views
I have a pair of read files where each is a mixed pool of reads from the Linked-read technology and Illumina short-read technology. Any suggestion on…
NGS clc-genomics illumina WGS
updated 7 months ago by 43k • written 7 months ago by ▴ 30
3
votes
9
replies
1.7k
views
How to get negative training set if I don't know what constitutes negative?
machine-learning dna-sequence blast
updated 6 months ago by 43k • written 7.7 years ago by • 0
3
votes
1
reply
439
views
How to BLAST a FASTA sequence with unknown organism source
chrZ BLAST FASTA
updated 7 months ago by 21k • written 7 months ago by • 0
3
votes
5
replies
343
views
Generating mpileup file using samtools
mpileup samtools
updated 14 days ago by 21k • written 14 days 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
3
votes
4
replies
695
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR volcano plotting R plot
updated 5 months ago by ★ 1.6k • written 5 months ago by ▴ 270
3
votes
3
replies
269
views
Gene Specific coverage from WGS data
WGS SARS-CoV2
updated 4 days ago by 43k • written 17 days ago by • 0
3
votes
3
replies
533
views
How to add value of column to barchart on hover?
R ggplot ggplotLy
updated 8 months ago by ★ 1.8k • written 8 months ago by ▴ 10
3
votes
1
reply
294
views
how to change the gene header names in a fasta file?
fasta bioawk awk seqkit
updated 5 weeks ago by 43k • written 5 weeks ago by • 0
3
votes
8
replies
656
views
Huge decrease of BUS records using bustools
single-cell bustools 10X
11 weeks ago by julien.wollbrett • 0
3
votes
2
replies
473
views
Program for Overlapping DMRs (Differentially Methylated Regions) Between Groups
methylation DMR
updated 7 months ago by ★ 2.0k • written 7 months ago by • 0
3
votes
4
replies
368
views
What should be used as a "baseline" in pooled CRISPR screen?
CRISPR MAGECK FACS
10 weeks ago by Aleksandr ▴ 10
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
3
votes
2
replies
191
views
Publish a Letter in higher impact vs Research article in lower impact
Article Letter Journal
updated 4 days ago by 82k • written 4 days ago by • 0
3
votes
16
replies
12k
views
combining z-scores into a single z-score value
excel R statistics
updated 11 months ago by 43k • written 5.2 years ago by ▴ 60
1,000 results • Page 5 of 20
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Recent Replies
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…
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.
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