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121,919 results • Page 705 of 2439
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0
votes
0
replies
800
views
Using Dgenies from the command line
dgenies alignment
4.6 years ago by langziv ▴ 70
2
votes
5
replies
1.7k
views
Annotating reads with the name of the feature to which they map
RNA-Seq
updated 4.6 years ago by ★ 2.7k • written 4.6 years ago by ▴ 20
0
votes
0
replies
618
views
How to compare two column from two files with specific condition in awk
awk text-processing
updated 4.6 years ago by 21k • written 4.6 years ago by • 0
1
vote
3
replies
2.0k
views
What tools do you use to find the potential off-target sites when designing Cas9/Cas12 RNA-guided endonucleases?
CRISPR off-target alignment
4.6 years ago by genomics0101 ▴ 10
0
votes
4
replies
7.0k
views
Link two proteins in Pymol
pymol link proteins
4.6 years ago by Hansen_869 ▴ 80
0
votes
0
replies
563
views
finding coverage of particular gene sequence from illumina short reads
coverage illumina
4.6 years ago by rthapa ▴ 90
1
vote
2
replies
7.2k
views
Error in reading MatrixMarket file format using Seurat Read10X
RNA-Seq 10x Seurat
updated 4.6 years ago by ★ 8.3k • written 4.6 years ago by ▴ 10
3
votes
3
replies
1.4k
views
probability of observing overlap between sets of genes
R
updated 4.6 years ago by 20 • written 6.1 years ago by ★ 2.6k
1
vote
1
reply
986
views
voomWithDreamWeights() has missing "NA" wheights for last samples
voomWithDreamWeights dream variaincePartition
4.6 years ago by RNAseqer ▴ 280
0
votes
0
replies
1.2k
views
Analyzing RNA-Seq with duplicate ensembl ids using DESeq2: should tximport be used?
RNA-Seq alignment R
4.6 years ago by Ridha ▴ 130
2
votes
4
replies
3.3k
views
F1 Score of Recursive Feature Elimination (RFE) Top 20 features Greater than RFE Cross Validation (CV) F1 Score
sklearn rfe rfecv f1score randomforests
4.6 years ago by ivnnvi • 0
0
votes
0
replies
1.1k
views
How to import a phylogenetic tree (in nexus format) with node support values in R
phylogeny R tree nexus
4.6 years ago by diversitree ▴ 10
2
votes
4
replies
1.9k
views
possible to convert hg19 coordinated position to hg38 coordinated position??
genome snp gene sequencing
updated 4.6 years ago by ★ 4.8k • written 4.6 years ago by ▴ 10
2
votes
0
replies
785
views
Forum: Need recommendations on best certificates to take to boost bioinformatics career and income.
courses
updated 2.5 years ago by 45k • written 4.6 years ago by ▴ 20
0
votes
2
replies
822
views
getting fastq ID with SNPs
SNP genome browser fastq
4.6 years ago by bitpir ▴ 250
3
votes
2
replies
849
views
Identifying cancer subtypes
RNA-Seq gene
updated 4.6 years ago by 20 • written 4.6 years ago by ▴ 320
0
votes
0
replies
1.1k
views
GATK4 BaseRecalibrator in Galaxy
Galaxy Variant Calling GATK4 BQSR BaseRecalibrator
4.6 years ago by jhy ▴ 10
0
votes
0
replies
762
views
Mapping long RNAseq reads to genome with nextGenMap - how to adjust parameters?
RNA-Seq
4.6 years ago by lechu ▴ 20
2
votes
8
replies
7.2k
views
Heatmap from EdgeR results
edgeR heatmaps DGEList CPM
updated 4.6 years ago by ★ 8.3k • written 4.6 years ago by ▴ 20
0
votes
1
reply
1.1k
views
Hardy-Weinberg equilibrium and GWAS in a livestock species (advice)
HWE GWAS
updated 4.6 years ago by ▴ 890 • written 4.6 years ago by • 0
0
votes
0
replies
885
views
How to visualize sequence annotation results from Trinotate
Trinotate
4.6 years ago by Kash ▴ 110
0
votes
2
replies
1.6k
views
Segmentation fault while running muscle
alignment gene software error
4.6 years ago by alicecol ▴ 20
0
votes
0
replies
1.3k
views
Question about ENCODE ATAC-seq bed file, bed narrowPeak vs bed idr_ranked_peak
ATAC-seq
4.6 years ago by yanweng ▴ 80
4
votes
3
replies
862
views
De novo transcriptome assembly
RNA-Seq
updated 4.6 years ago by ★ 30k • written 4.6 years ago by • 0
3
votes
2
replies
1.1k
views
Expanding gene family using hmmer
hmmer jackhmmer sequence homology
updated 4.6 years ago by ★ 30k • written 4.6 years ago by ▴ 80
2
votes
2
replies
2.4k
views
Snakemake (MissingOutputException) doesn't seem to find output files.
Snakemake
4.6 years ago by jkim ▴ 220
0
votes
0
replies
709
views
How do I calculate linkage disequilibrium in 4 mixed ancestry individuals?
SNP genome Linkage disequilibrium Plink
updated 4.6 years ago by 20 • written 4.6 years ago by • 0
1
vote
4
replies
1.0k
views
Group Difference Non-parametric test
R nonparametrictest biostatistics
updated 4.6 years ago by ▴ 10 • written 4.6 years ago by • 0
2
votes
3
replies
4.0k
views
R object can allow duplicated column name and storing different types of values
R python
updated 4.6 years ago by 45k • written 4.6 years ago by ▴ 40
0
votes
4
replies
2.3k
views
dotplot for multifasta files
dotplot multifasta
4.6 years ago by agata88 ▴ 870
0
votes
0
replies
690
views
What are some nice plots that can be generated from a Gene Rgulatory Network (GRN) ?
GRN R
4.6 years ago by donnieDarko • 0
0
votes
0
replies
868
views
News: Three x 2day online Python courses
Python
updated 2.6 years ago by 45k • written 4.6 years ago by ▴ 60
0
votes
0
replies
865
views
News: Nine x 2day online R courses
R
updated 2.6 years ago by 45k • written 4.6 years ago by ▴ 60
0
votes
0
replies
863
views
DEG analysis between control and treatment groups in integrated scRNAseq analysis
scRNAseq integration DEG
4.6 years ago by aa123 • 0
0
votes
1
reply
701
views
Genomics tools - gene indentification from AA sequence
sequence sequencing alignment genome
updated 4.6 years ago by 13k • written 4.6 years ago by • 0
1
vote
1
reply
900
views
Batch-correction of partially confounded RNA-seq data
RNA-Seq
updated 4.6 years ago by 9.0k • written 4.6 years ago by ★ 3.5k
11
votes
8
replies
4.9k
views
How to sort fasta file numerically
Assembly genome sequence
updated 4.6 years ago by 89k • written 4.6 years ago by ▴ 540
0
votes
0
replies
648
views
How to produce SNP/Indel markers On IGV using differentially expressed genes?
snp indel igv DEG Markers
4.6 years ago by mr.ank2999 • 0
3
votes
4
replies
4.2k
views
what the difference between "translated cds" and "protein"
sequence gene genome
updated 4.6 years ago by 103k • written 4.6 years ago by ▴ 30
1
vote
2
replies
2.5k
views
Alignment of assembly on reference genome with MiniMap2 returns false unmapped contig
assembly alignment MiniMap2
updated 4.6 years ago by 35k • written 4.6 years ago by ▴ 10
9
votes
8
replies
7.8k
views
8 follow
Is there a software that can compare phylogenetic trees to each othe (face to face comparison)?
comparison visualization tree phylogenetics
updated 2.2 years ago by ▴ 10 • written 10.6 years ago by ▴ 10
0
votes
0
replies
606
views
How to re-annotate chloroplast genome
re-annotate chloroplast
4.6 years ago by aggeliki.panetsou • 0
0
votes
0
replies
543
views
How to set different themes between the panels of RStudio
R
4.6 years ago by Fede_Santos95 ▴ 20
7
votes
6
replies
2.0k
views
Download Microarray GSE files GEO
R microarray getGEO
updated 3.2 years ago by ★ 1.3k • written 4.6 years ago by ▴ 20
0
votes
0
replies
593
views
How many variant caller is needed for somatic mutations?
SNP variant caller
4.6 years ago by whb ▴ 60
1
vote
0
replies
912
views
Tumour mutation burden vs mutant cells ratio vs Variant allele fraction
vaf maf tmb
4.6 years ago by whb ▴ 60
0
votes
0
replies
697
views
mitochondrial tRNA secondary stracture / model fold
trnas mitochondria stracture
4.6 years ago by blur ▴ 280
0
votes
3
replies
1.5k
views
Use multiprocessing from within a PyMOL plugin
pymol multithreads multiprocessing pymol plugin
4.6 years ago by d.s.molodenskiy • 0
0
votes
0
replies
1.2k
views
How RNAseq input file for ssGSAE should be normalized?
VST ssGSEA normalization
4.2 years ago by Raheleh ▴ 260
0
votes
0
replies
598
views
Is the optimal model found by IQ-tree software used in raxml software to build ML tree?
IQ-tree raxml
4.6 years ago by Daier ▴ 20
121,919 results • Page 705 of 2439
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Answer: [vg giraffe] Unable to add read group to BAM file
Comment: [vg giraffe] Unable to add read group to BAM file
Answer: [vg giraffe] Unable to add read group to BAM file
Answer: vcf multisample
Answer: vcf multisample
Answer: vcf multisample
Answer: Different UMAP for batch correction in R and Pytho
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Recent Replies
Comment: Help with species tree with orthofinder, iqtree and branch labeling by GenoMax 153k
> I don’t have clear species labels in my headers, only sequence IDs. I have not used iqtree, so this is only a thought ... should it be y…
Comment: Help with species tree with orthofinder, iqtree and branch labeling by san96 ▴ 190
Thank you so much.
Comment: [vg giraffe] Unable to add read group to BAM file by saruman ▴ 10
Yes, it seems so. Thank you.
Comment: cellranger mkref fail/error by GenoMax 153k
> The thing is that I do not have a genome for these organisms. That is not what `cellranger mkref` is expecting. You could consider alt…
Comment: cellranger mkref fail/error by tatsispolychronis • 0
The thing is that I do not have a genome for these organisms. i made a transcriptome using TRinity and this is what I am feeding it. I do n…
Comment: Genome Assembly QC from BAM files by SomeOne ▴ 240
Hi, I am not sure if i can call them good assemblies. Although based on QUAST and BUSCO stats, everything looks too good but somehow i hav…
Comment: cellranger mkref fail/error by GenoMax 153k
You need to provide the genome reference for the `--fasta` option as noted in https://www.10xgenomics.com/support/software/cell-ranger/late…
Answer: Methods to analyse structural similarity: co-evolution vs convergence by Joe 22k
Without historical data (ancient DNA) there's no way to ever really know this for certain. The best we can do is make inferences based on t…
Answer: vcf multisample by Pierre Lindenbaum 166k
eg : https://ega-archive.org/datasets/EGAD50000001683 > Merged VCF file from sporadic Meniere disease cohort (found using https://dat…
Comment: Genome Assembly QC from BAM files by GenoMax 153k
Since this saga has been on going for a long time, it will be helpful to add a comment as to how you finally got to this point of what seem…
Comment: Methods to analyse structural similarity: co-evolution vs convergence by dthorbur ★ 3.1k
A few comments. 1. Coevolution of a trait between 2 organisms can end up with a convergent structure with another organism. It's not e…
Comment: Genome Assembly QC from BAM files by SomeOne ▴ 240
Thank you. Based on the description these two look really what i wanted to see.
Comment: miRNA low mapping ratings by i.sudbery 22k
Also, can you just clarify that the output above is from cutadapt or form miRDeep2?
Comment: miRNA low mapping ratings by i.sudbery 22k
What happens if you remove the `--minimum-length` requirement to cutadapt, and then run fastqc on the result - what size disitribution do y…
Answer: Genome Assembly QC from BAM files by colindaven 7.9k
You can have a look at the tools in the PAQman pipeline https://github.com/SAMtoBAM/PAQman, and maybe also Inspector https://github.com/Mag…
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