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757 results • Page 5 of 16
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2
votes
1
reply
338
views
Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
shotgun metagenomics blastp taxonomy
updated 28 days ago by 142k • written 28 days ago by • 0
2
votes
5
replies
411
views
Importing a fastq file
Fastq
updated 8 days ago by ▴ 120 • written 8 days ago by • 0
2
votes
5
replies
269
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 4 days ago by 8.5k • written 4 days ago by • 0
2
votes
11
replies
1.0k
views
Questions about a bug when transferring cram file to bam file
sequence samtools bcftools
updated 18 days ago by ★ 1.2k • written 4 weeks ago by • 0
2
votes
8
replies
380
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
2
votes
2
replies
1.0k
views
Batch correct batch 2 while leaving batch 1 unchanged.
limma machine-learning batch-effect
updated 29 days ago by 43k • written 3.8 years ago by 19k
2
votes
5
replies
10k
views
Find Corresponding Author: Doi Metadata?
updated 26 days ago by 43k • written 10.6 years ago by ▴ 150
2
votes
6
replies
387
views
BWA alignment
Samtools bam
updated 2 days ago by ▴ 260 • written 5 days ago by • 0
2
votes
2
replies
315
views
p-value in CIBERSORT
CIBERSORT p-value
16 days ago by michelafrancesconi9 ▴ 20
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
2
votes
4
replies
720
views
Count all variants from vcf file
variants vcf Count
updated 10 days ago by 161k • written 21 months ago by • 0
2
votes
3
replies
998
views
Method to detect genome doubling
CNV genome doubling
updated 25 days ago by 4.2k • written 4.5 years ago by ▴ 750
2
votes
1
reply
2.1k
views
How to make batch univariate cox analysis for list
univariate-cox-analysis
updated 29 days ago by 43k • written 4.8 years ago by ▴ 20
2
votes
3
replies
327
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus annotation assembly genome
updated 14 days ago by ★ 2.0k • written 14 days ago by ▴ 30
2
votes
5
replies
2.5k
views
identifying transgene insertion site in WGS
WGS insertion site trangene de-novo soap
updated 9 days ago by • 0 • written 5.1 years ago by ★ 1.8k
2
votes
4
replies
2.5k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi metagenomics centrifuge gi_taxid_nucl.dmp taxonomy
updated 23 days ago by • 0 • written 2.5 years ago by • 0
2
votes
5
replies
954
views
Retrieval of Active site information programmatically
Catalytic Python Active PDB site Site
updated 18 days ago by ★ 2.0k • written 2.1 years ago by • 0
2
votes
3
replies
504
views
Sheep reference genome remapping coordinates
reference remap sheep coordinates genome
29 days ago by valentinatsar • 0
2
votes
5
replies
645
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis MEGA
updated 27 days ago by ★ 27k • written 28 days ago by • 0
2
votes
2
replies
482
views
Using vg gamsort with naive sorting algorithm
gamsort vg
updated 24 days ago by 161k • written 8 months ago by ▴ 80
2
votes
2
replies
1.6k
views
Combining control samples from 2 separate studies. Model matrix for batch effect?
gene-expression R limma batch-effect model-matrix
updated 29 days ago by 43k • written 7.3 years ago by ▴ 20
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
2
votes
3
replies
383
views
clustalo - align milions of short seq, memory issue
memory clustalo
updated 25 days ago by ★ 27k • written 25 days ago by ▴ 120
2
votes
3
replies
339
views
Problem with Seurat package in PercentageFeatureSet function
cell single
updated 8 days ago by ★ 2.5k • written 12 days ago by ▴ 60
2
votes
2
replies
244
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly BWA-MEM2 Hi-C
updated 18 days ago by 142k • written 19 days ago by • 0
2
votes
4
replies
337
views
from row count to tpm
tpm row-count normalization
updated 17 days ago by 43k • written 25 days ago by ▴ 20
2
votes
2
replies
350
views
Association study using SNP data
Association Allele Parentage SNP
12 days ago by drajangirija • 0
2
votes
5
replies
426
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq assembly transcriptome contamination
21 days ago by Lada ▴ 30
2
votes
4
replies
392
views
Should I use unpaired reads from trimmomatic
RNA-seq QC Trimmomatic
updated 24 days ago by 14k • written 25 days ago by • 0
2
votes
4
replies
415
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
24 days ago by HyperEvo • 0
1
vote
1
reply
189
views
Including plasmid in alignment
Bacteria Transcriptomics BOWTIE2 STAR
17 days ago by heelpPlease • 0
1
vote
3
replies
327
views
TaxID mapping file
annotation blobtools RNAseq decontamination transcriptomes
12 days ago by Lada ▴ 30
1
vote
8
replies
396
views
Overlapping Ranges within Granges object
Genomicranges IRanges GRanges
updated 11 minutes ago by 35k • written 4 days ago by ▴ 60
1
vote
4
replies
502
views
cellranger error message
multiplexing cellranger
updated 7 days ago by • 0 • written 3 months ago by ▴ 10
1
vote
3
replies
282
views
DiffBind: no peaks in DBA
MACS2 DiffBind ChIP-seq
updated 15 days ago by ★ 16k • written 15 days ago by ▴ 10
1
vote
1
reply
175
views
student
epitranscriptomics
updated 10 days ago by 82k • written 10 days ago by • 0
1
vote
1
reply
411
views
Problem with Mirdeep2 and Randfold output
mirdeep2 Randfold
29 days ago by otieno43 ▴ 30
1
vote
6
replies
728
views
anRichment is missing
WGCNA anRichment
updated 11 days ago by 142k • written 6 months ago by ▴ 180
1
vote
1
reply
257
views
Adjust pvalue in R with different approach give me all different outcome
statistics R p-value
updated 17 days ago by 43k • written 17 days ago by ▴ 60
1
vote
4
replies
346
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus annotation assembly genome
updated 3 days ago by 8.6k • written 4 days ago by ▴ 30
1
vote
2
replies
278
views
News: We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
cell-clustering Spatial-transcriptomics
updated 10 days ago by • 0 • written 11 days ago by ▴ 10
1
vote
7
replies
541
views
Question regarding WGCNA
WGCNA Network-construction
8 days ago by deepak • 0
1
vote
0
replies
2.1k
views
Tool: DASC -- detecting hidden batch effects in gene expression datasets (Array/RNA-Seq/scRNA-Seq)
RNA-Seq scRNA-Seq R Batch-Effect
updated 29 days ago by 43k • written 6.9 years ago by ★ 1.1k
1
vote
2
replies
225
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart RNAseq kallisto
1 day ago by bioinfo ▴ 150
1
vote
0
replies
105
views
News: Course on Manual Genome Curation
Genome-Assembly Pretext-View Manual-Genome-Curation
updated 1 day ago by 43k • written 1 day ago by ★ 2.5k
1
vote
7
replies
503
views
Downsampling long-read BAM files
nanopore BAM QC ONT downsampling
14 days ago by eebloom ▴ 80
1
vote
1
reply
214
views
Failed kmer content
kmer illumina ngs
updated 24 days ago by 43k • written 24 days ago by • 0
1
vote
10
replies
889
views
error to run rnammer
phylogenomics rRNA_extraction rnammer
updated 11 days ago by • 0 • written 4 months ago by ▴ 30
1
vote
1
reply
304
views
Removing Illumina microarray probes with no expression HumanHT-12v4
microarray HumanHT-12v4 Illumina
updated 27 days ago by ★ 7.2k • written 28 days ago by • 0
1
vote
2
replies
457
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics bootstrap
9 days ago by Zeng Hao ▴ 40
757 results • Page 5 of 16
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How can I perform Differential expression analysis with just one control and one cancer sample?
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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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