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121,991 results • Page 258 of 2440
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496
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How to load inidividual ADT and RNA data to the same AnnData structure
python CITE-seq Scanpy
updated 2.4 years ago by 45k • written 2.4 years ago by • 0
6
votes
4
replies
1.5k
views
Problematic experimental design RNA-Seq
RNA-Seq
updated 2.4 years ago by 89k • written 2.4 years ago by ★ 2.6k
0
votes
0
replies
896
views
Job: Ph.D. Student in Computational Biology and Machine Learning at SciLifeLab, Stockholm
Proteomics Mass-spectrometry Machine-Learning Computational-Biology
2.4 years ago by lukas.kall ▴ 40
2
votes
1
reply
765
views
How to analyze mars-seq single end-read scRNAseq data?
cellranger single-end scRNAseq
updated 2.4 years ago by 89k • written 2.4 years ago by ▴ 20
0
votes
2
replies
1.1k
views
Mapping reads to a multifasta reference
multifasta map
updated 2.4 years ago by 48k • written 2.4 years ago by • 0
0
votes
0
replies
536
views
Is it valid to use UMI-based analysis pipelines for aptamer-based proteomics
UMI aptamer RNA-seq proteomics
2.4 years ago by Ali • 0
2
votes
1
reply
1.1k
views
Generate hashes for all sequences in a FASTA file
stringtie RNA hash
updated 2.4 years ago by 154k • written 2.4 years ago by ▴ 20
0
votes
0
replies
897
views
Tool: Single-cell RNA-seq data analysis tool Cellenics®
single-cell RNA-seq scRNA-seq
updated 2.4 years ago by 45k • written 2.4 years ago by • 0
0
votes
7
replies
3.9k
views
Nanopore config files
nanopore longread
2.4 years ago by kenneditodd ▴ 50
1
vote
1
reply
958
views
IGV custom tracks from gff3 files; how to customize feature blocks "shape"?
visualization gff3 igv
updated 2.4 years ago by 166k • written 2.4 years ago by ▴ 60
0
votes
2
replies
1.0k
views
clusterprofile enrichment analysis
enrichment analysis clusterprofile
updated 2.4 years ago by ★ 2.0k • written 2.4 years ago by • 0
0
votes
2
replies
1.4k
views
When there are multiple runs within a single experiment (in RNA-seq analysis)
runs experiments RNAseq SRA Illumina
updated 2.4 years ago by 154k • written 2.4 years ago by ▴ 40
1
vote
1
reply
831
views
SnpEff Error
snpEff
updated 2.4 years ago by 166k • written 2.4 years ago by ▴ 30
0
votes
1
reply
938
views
hierarchical clustering heatmap with r
R
updated 2.4 years ago by 6.2k • written 2.4 years ago by ▴ 20
1
vote
6
replies
4.3k
views
How to extract alignments with 0 mismatch from sam or bam file by using samtools?
bam samtools sam
updated 2.4 years ago by • 0 • written 4.4 years ago by • 0
0
votes
0
replies
653
views
single cell RNA analysis in python
cell single python
2.4 years ago by sooni ▴ 20
2
votes
1
reply
1.4k
views
coef /makeContrasts very different results
makeContrasts coef2 edgeR
updated 2.4 years ago by ★ 8.3k • written 2.5 years ago by ▴ 280
3
votes
9
replies
3.7k
views
How to extract summary statistics from GFF3 /GTF file?
gff3 gene-annotation summary-statistics
updated 2.4 years ago by 9.3k • written 2.4 years ago by • 0
0
votes
0
replies
444
views
How to see gene names in goProfiler2 functional enrichment analysis
goProfiler2 enrichment GO clusterprofiler
2.4 years ago by Zhujunnn • 0
1
vote
1
reply
1.2k
views
DSSP (MMCIF) output to .ss8 file format
structure secondary dssp
2.4 years ago by Ivan • 0
1
vote
7
replies
2.4k
views
Accuracy of Methods for Gene Variant Detection and Quantification: Kallisto Pseudoalignment vs. STAR Alignment
kallisto STAR RNA-seq Transcript_variants
2.4 years ago by sohail.mbio • 0
0
votes
2
replies
2.6k
views
vg deconstruct: how can I generate a VCF (in hg38 coords) of differences between hg38 and CHM13?
variant-graph vg
updated 2.4 years ago by ▴ 850 • written 2.4 years ago by ▴ 10
0
votes
0
replies
803
views
Job: PostDoc in Computational Biology at Leibniz Institute for Environmental Medicine
NGS Evolution Omics Aging
2.4 years ago by Arne.Sahm • 0
4
votes
6
replies
1.4k
views
how to plot SV(structural variants) from many assemblies of a given locus
SV
2.4 years ago by natalev ▴ 20
6
votes
17
replies
3.0k
views
Filtering rows based on a list if all the entries of the list correspond to a specific row value
row-matching sorting filtering
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 10
2
votes
0
replies
520
views
How to annotate clusters with one cell type?
scRNA Seurat Cluster SingleR annotation
2.4 years ago by Bioinfo ▴ 30
2
votes
1
reply
3.7k
views
cellranger count: an extremely low rate of correct barcodes was observed
cellranger scRNAseq
updated 2.4 years ago by 154k • written 2.4 years ago by ▴ 20
1
vote
2
replies
990
views
multi-mapping reads settings in Rsubread or Rsubjunc
Rsubjunc RNA-seq
2.4 years ago by xiaoleiusc ▴ 140
1
vote
3
replies
1.0k
views
Where to upload and store annotated genetic variant data online?
mutation annotated cancer database variant
updated 2.4 years ago by 154k • written 2.4 years ago by ▴ 20
0
votes
1
reply
861
views
Diverse sampling from MSA / phylogenetic tree?
clustering proteins sampling alignment msa
updated 2.4 years ago by ▴ 880 • written 2.4 years ago by ▴ 40
2
votes
4
replies
1.9k
views
Different total number of sequences between the two PE fastq files
NGS RNA-Seq Paired-End
updated 2.4 years ago by 154k • written 2.4 years ago by • 0
0
votes
0
replies
916
views
How the "IJC" is calculated in rMATS tool?
Sashimi sequencing alignment rMATS rna-seq
2.4 years ago by Apex92 ▴ 320
4
votes
8
replies
3.7k
views
Error while running nf-core/rnaseq pipeline
nf-core RNA-seq
2.4 years ago by eesha28112001 • 0
2
votes
6
replies
1.5k
views
Find data-based Gene_IDs for unknown gene_IDs in gtf.file
RNA-SEQ annotation GO-term
2.4 years ago by Pegasus ▴ 130
0
votes
0
replies
497
views
The non-synonymous/synonymous rate ratio for test in datamonky represents the dn-ds of the entire gene ?
evolution datamonky SLAC Positive selection
2.4 years ago by ly887554221 • 0
6
votes
12
replies
3.9k
views
Help with error in cellranger
Cellranger
updated 2.4 years ago by 154k • written 2.4 years ago by ▴ 360
0
votes
2
replies
6.2k
views
Removing specific cluster based on one gene down regulation
Single-cell Seurat scRNA-seq
updated 2.4 years ago by ▴ 850 • written 2.4 years ago by • 0
0
votes
1
reply
6.2k
views
Seurat scRNA convert Ensembl ID to gene symbol
ensembl genesymbol seurat
updated 2.4 years ago by ▴ 850 • written 2.4 years ago by • 0
0
votes
7
replies
3.1k
views
How can I speed up wget from UniProt for UniRef90/50 fasta?
wget download uniprot uniref
updated 2.4 years ago by ★ 30k • written 2.4 years ago by ▴ 750
3
votes
6
replies
2.3k
views
Edit and re-head BAM file
samtools BAM
updated 2.3 years ago by 45k • written 2.4 years ago by ▴ 130
0
votes
2
replies
1.0k
views
How to analyze GO term
GO
updated 2.4 years ago by ▴ 470 • written 2.4 years ago by • 0
2
votes
3
replies
1.5k
views
Haplotype specific alleles
freuqency bam haplotype
2.4 years ago by Korsocius ▴ 270
3
votes
2
replies
2.0k
views
Modeltest-ng and MrBayes
Modeltest model phylogenetics Mrbayes selection
2.3 years ago by Francisco Pina Martins • 0
3
votes
2
replies
1.5k
views
Salmon for RNAseq alignement?
RNASeq Salmon bacteria
updated 2.4 years ago by ★ 2.4k • written 2.4 years ago by • 0
6
votes
1
reply
1.2k
views
How to determine if any samples are outliers in PCA? What is the criteria?
PCA
updated 2.4 years ago by 27k • written 2.4 years ago by ▴ 10
0
votes
8
replies
2.5k
views
Error in champ.load() function
ChAMP
updated 2.4 years ago by ★ 2.1k • written 2.4 years ago by • 0
1
vote
4
replies
1.3k
views
Bacterial metatransciptome antimicrobial resistance genes workflow?
RNAseq metatranscriptomics
2.4 years ago by SushiRoll ▴ 140
0
votes
0
replies
616
views
EIGENSOFT mergeit without family names
mergeit EIGENSOFT familynames
2.4 years ago by Inez • 0
3
votes
6
replies
1.9k
views
How to get the gene ID
transcriptID geneID
2.4 years ago by kapbermudez • 0
1
vote
2
replies
847
views
Building phylogenetic tree accounting for spatial information
BEAST IQ-TREE COVID-19
2.4 years ago by vembha • 0
121,991 results • Page 258 of 2440
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Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
Answer: TMM-Normalization
Answer: Tools to simulate Illumina short read sequences and ONT long reads with a refere
Answer: Tools to simulate Illumina short read sequences and ONT long reads with a refere
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Answer: Difficulty running FoldX in linux by Mensur Dlakic ★ 30k
The post looks much better now, so you did something. The preview here works fine. It simply can't be that the preview for your original po…
Comment: GUI commercial software for 10x single cell gene expression analysis by GenoMax 154k
Black box software has its cons but in instances like what OP needs that may be the only viable option. Their use limits reproducibility as…
Comment: downloading raw bam files from pacbio sequencer by GenoMax 154k
Have you checked : https://www.pacb.com/connect/datasets/
Comment: TMM-Normalization by kalavattam ▴ 380
No, but a modified version of TMM does: “GeTMM.” See the paper [here](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-0…
Comment: Difficulty running FoldX in linux by strayeroliver • 0
Responding to your answer. - I spent a lot of time formatting it just right, using the ``` methodology you mentioned. It looks very good o…
Comment: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions by Phil Ewels ★ 1.5k
Found the docs: https://www.nextflow.io/docs/latest/process.html#multiple-input-files | Arity | Name pattern | Staged file names | |---|--…
Comment: Dorado in PowerShell on Windows by jared.andrews07 ★ 19k
No more than running it on native Linux (as that's what WSL is at this point).
Answer: SNP calling ONT sequenced files by colindaven 8.0k
The quality of (modern, SUP basecalled, but certainly not fast basecalled) ONT sequences should be fine, especially for bacterial SNP call…
Comment: SNP calling ONT sequenced files by GenoMax 154k
What is the median length of raw reads and how many do you have? Has the data been basecalled with "high" or "super" accuracy? > I have …
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere by GenoMax 154k
This question is about simulating reads and not read mapping.
Comment: GUI commercial software for 10x single cell gene expression analysis by yura.grabovska ▴ 830
I have fun memories of month-long discussions with Illumina support about their GenomeStudio methylation module asking them to provide info…
Comment: scVI vs Harmony, which is better for cell type based clustering in brain tissue? by Arup Ghosh 3.4k
Try the references from the following publications. https://www.nature.com/articles/s41591-024-03150-z https://www.science.org/doi/10.112…
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions by Phil Ewels ★ 1.5k
There's an easier way than manually renaming the output files (though you can do this, and it works) - you can use the `name` (aka `stageAs…
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Last Call for this event. Apply now, if you like to join.
Comment: Difficulty running FoldX in linux by Mensur Dlakic ★ 30k
The program is definitely working. It doesn't matter that it didn't produce `TER` and `END` lines at the end. Those are optional in PDB fil…
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