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121,926 results • Page 91 of 2439
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5
votes
11
replies
2.6k
views
6 follow
Conversion of Gene Name to Ensembl ID
Ensembl RNA-Seq
updated 14 months ago by 4.8k • written 14 months ago by • 0
2
votes
17
replies
3.5k
views
RNA STAR and trimming
trimming STAR RNA-seq RNA
updated 14 months ago by 153k • written 14 months ago by ▴ 10
5
votes
8
replies
2.8k
views
How to reassign the orientation of clusters in pheatmap
R pheatmap heatmap
14 months ago by Meghan.T ▴ 10
0
votes
0
replies
450
views
Training a Mini Calico/Borzoi Model using cardiomyocyte RNA-Seq, ATAC-Seq, and WGBS
Borzoi WGBS Calico RNA-Seq ATAC
updated 14 months ago by 45k • written 14 months ago by • 0
0
votes
0
replies
366
views
small scale of perb_score in the output from scRank and order of the rank
scRank
updated 14 months ago by 45k • written 14 months ago by ▴ 40
2
votes
10
replies
1.6k
views
Extracting unmapped reads from a sam file and converting to fastq
samtools
updated 14 months ago by 45k • written 14 months ago by • 0
0
votes
0
replies
465
views
News: Course: RADseq data analysis using Stacks (online)
RAD-seq Genomics Stacks Phylogenomics Population
updated 14 months ago by 45k • written 14 months ago by ★ 2.6k
0
votes
3
replies
785
views
Mageck NEST cannot find control genes/sgRNAs
python mageck crispr-screen
updated 14 months ago by 153k • written 14 months ago by • 0
0
votes
0
replies
334
views
How do I bin my individually assembled metagenome samples
Metagenome Binning
updated 14 months ago by 45k • written 14 months ago by • 0
5
votes
4
replies
1.6k
views
Multiple same UMI's mapped to the same cell with different sequence
10x UMI BAM scRNAseq Barcode
14 months ago by zbidav ▴ 30
0
votes
0
replies
499
views
Minfi - bumphunter M and Beta values
Minfi methylation bumphunter
14 months ago by Eren • 0
0
votes
2
replies
644
views
Get SYMBOL using mapIds with T2T genome ?
t2t
14 months ago by Picasa ▴ 690
0
votes
1
reply
543
views
HUB gene selection
HUB-gene
updated 14 months ago by • 0 • written 14 months ago by • 0
0
votes
0
replies
372
views
CNV calling with complex genomic background
CNV
14 months ago by 雨辰 • 0
6
votes
4
replies
1.5k
views
Forum: Resume building projects to break into bioinformatics?
job-hunting career-change
updated 12 months ago by ★ 2.1k • written 14 months ago by ▴ 20
4
votes
1
reply
642
views
combine two density plots in one plot
R ggplot2 density_plot
updated 14 months ago by 12k • written 14 months ago by ▴ 60
0
votes
1
reply
954
views
Trinotate generates an empty report, only headers and no data inside
trinotate metatranscriptome docker
updated 14 months ago by • 0 • written 14 months ago by • 0
2
votes
0
replies
306
views
merge-methcounts sites not sorted error
methpipe methylation
updated 14 months ago by 45k • written 14 months ago by ▴ 20
0
votes
0
replies
477
views
Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
MAST differential-expression lmer
updated 14 months ago by 45k • written 14 months ago by ▴ 420
0
votes
1
reply
1.6k
views
Xenium multi sample data
Xenium batch-effect annotation
updated 14 months ago by 45k • written 16 months ago by ▴ 260
0
votes
0
replies
403
views
ggplot2 geom_density() density value estimates can be greater than 1?
R tpm density ggplot
14 months ago by Prawesh • 0
0
votes
0
replies
493
views
Job: PhD position Integrated Modeling
modeling gene-regulation machine-learning
updated 14 months ago by 45k • written 14 months ago by • 0
0
votes
2
replies
668
views
gene prediction
potato gene-prediction qingshu9
14 months ago by zhu • 0
0
votes
0
replies
371
views
generating a genome reference fasta file
FASTA BAM reference
updated 14 months ago by 45k • written 14 months ago by ▴ 60
4
votes
6
replies
1.7k
views
More than 90% of variants were failed to match, using LiftoverVcf of Picard.
Liftover LiftoverVcf picard
14 months ago by yoshidakoki • 0
0
votes
2
replies
551
views
MAXLFQ peptide data analysis
chemoproteomics proteomics MAXLFQ
14 months ago by SHN ▴ 40
1
vote
4
replies
1.6k
views
Minimap2 mapping problem
amplicon reference minimap2 mapping haplotype
14 months ago by Maximilian ▴ 10
0
votes
0
replies
469
views
Clustering single-cell CNV data
R clustering infercnv CNV scRNA
14 months ago by yura.grabovska ▴ 820
0
votes
2
replies
937
views
BUSCO did not find any match. Retraining did not complete correctly. BUSCO analysis failed!
Augustus pipeline MAKER annotation BUSCO
updated 14 months ago by 153k • written 14 months ago by ▴ 20
0
votes
0
replies
338
views
How to identify the strongest eQTL for a gene in a specific tissue using GTEX?
eQTL GTEX GTEXv8
14 months ago by AAP • 0
0
votes
3
replies
697
views
Filterbytile.sh - Exception in thread "main" java.lang.RuntimeException: Can't read file ...
Illumina filterbytile Java RNA
updated 14 months ago by 153k • written 14 months ago by • 0
0
votes
5
replies
1.5k
views
Eukaryotic genome Assembly
Genome-assembly MaSuRCA
updated 14 months ago by 45k • written 14 months ago by ▴ 60
0
votes
0
replies
301
views
sounDMR DMR analysis package in R
sounDMR ASAP DMR_Analysis
14 months ago by praddyumnapdm • 0
0
votes
1
reply
1.0k
views
Deconvolution of RNAseq (bulk) from skin samples
RNAseq skin-references deconvolution
updated 14 months ago by • 0 • written 3.9 years ago by ▴ 10
0
votes
0
replies
374
views
DNA methylation and plot manhattan
dna_methylation plot manhattan
14 months ago by fatii0ma • 0
3
votes
8
replies
1.7k
views
Differential analysis of enrichment results
statistics enrichment
14 months ago by Aspire ▴ 390
1
vote
2
replies
1.5k
views
Forum: scRNA-seq: Do people eliminate housekeeping genes for the sake of increasing algorithmic efficiency (and this speed)?
housekeeping-genes scRNA-seq
updated 14 months ago by 45k • written 14 months ago by • 0
5
votes
5
replies
1.8k
views
best way to submit hpc job using snakemake
snakemake
14 months ago by QX ▴ 80
3
votes
1
reply
715
views
Batch correction between cancer only data and normal only data
methylation batch-effect
updated 14 months ago by 45k • written 14 months ago by • 0
0
votes
0
replies
313
views
Different methods of data normalisation produce different cluster markers
R DGE Seurat
updated 14 months ago by 12k • written 14 months ago by • 0
1
vote
0
replies
379
views
Removal of samples with weird log-CPM distribution or voomWithQualityWeights?
voomWithQualityWeights limma PCA outliers
14 months ago by t.fortunato.asquini ▴ 10
1
vote
1
reply
750
views
DESeq2 sizeFactor for Bacterial RNASeq
normalization bacteria rRNA RNASeq
updated 14 months ago by 15k • written 14 months ago by • 0
2
votes
2
replies
642
views
Basics: How do I generate a VCF file from a genome and annotate it with Clinvar
VCF Fastq Clinvar Annovar
updated 14 months ago by 7.9k • written 14 months ago by ▴ 10
1
vote
3
replies
850
views
Chimeric reads analysis
NGS
updated 14 months ago by 22k • written 14 months ago by ▴ 150
0
votes
0
replies
365
views
RepeatMasker without DNA transposons, satellites and SINEs
transposons DNA RepeatModeler RepeatMasker
14 months ago by san96 ▴ 190
8
votes
7
replies
4.8k
views
Ensembl Api: How To Print All Transcript Isoforms As A Multifasta Alignment
ensembl transcript isoform multiple fasta
updated 14 months ago by ★ 4.3k • written 14.3 years ago by ★ 5.1k
5
votes
6
replies
1.4k
views
Issue with converting Affy IDs to gene IDs/symbols
biomart affymetrix GEOquery microarray
updated 14 months ago by ▴ 820 • written 14 months ago by ▴ 420
2
votes
5
replies
1.2k
views
adjusting pheatmap based on common genes
RNA-seq heatmap
14 months ago by Meghan.T ▴ 10
0
votes
4
replies
1.0k
views
convert list to fasta format
python fasta
14 months ago by pinheirofabiano ▴ 130
0
votes
0
replies
392
views
Large insertion sequence reconstruction from paired-end sequenced sample BAM files
reconstruction
14 months ago by Qboy ▴ 10
121,926 results • Page 91 of 2439
Recent Votes
Comment: Restricting ncbi-genome-download (bacteria, viral, fungi, archaea, protozoa) to
Answer: Restricting ncbi-genome-download (bacteria, viral, fungi, archaea, protozoa) to
Comment: Genome Assembly QC from BAM files
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
Comment: cellranger mkref fail/error
gnomAD: query utilitites
Answer: How to overcome OS return value: 4 with SPAdes
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Recent Replies
Comment: Restricting ncbi-genome-download (bacteria, viral, fungi, archaea, protozoa) to by Mensur Dlakic ★ 30k
Always good to learn new things.
Comment: Restricting ncbi-genome-download (bacteria, viral, fungi, archaea, protozoa) to by GenoMax 153k
> I don't think there are any host links in NCBI records This information is not available for all genomes, but it is there for some of th…
Answer: Restricting ncbi-genome-download (bacteria, viral, fungi, archaea, protozoa) to by Mensur Dlakic ★ 30k
As you said, the package does not support the search for hosts. Furthermore, I don't think there are any host links in NCBI records, so it …
Answer: Restricting ncbi-genome-download (bacteria, viral, fungi, archaea, protozoa) to by GenoMax 153k
There may be a better answer, but let us start here. This is a two (or more step) solution using NCBI `datasets` ([**LINK**][1]). NOTE: I…
Answer: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by Vittorio • 0
Joining the convo a bit late, but I found it super useful since I am struggling to analyze MGI data myself. For the library prep used in th…
Comment: How to overcome OS return value: 4 with SPAdes by marongiu.luigi ▴ 760
Yep, that was it. I was using a G:-sync folder... Thank you.
Comment: Help with Model by i.sudbery 22k
There is no way to "code" this directly. Your problem is mathematics, not programming. Standard stochastic models deal with a set of sta…
Answer: How to overcome OS return value: 4 with SPAdes by GenoMax 153k
I am going to hazard a guess that the spaces and email address in file path (you may want to redact your email from post above) is causing …
Comment: Hifiasm is getting killed while trying to assemble a genome by GenoMax 153k
Are you trying to reproduce the assembly result? If not, the complete assembly is already available at NCBI: https://www.ncbi.nlm.nih.gov…
Comment: Genome Assembly QC from BAM files by GenoMax 153k
This may be another example where the assembly you obtained may be better than an existing one .. certainly as far as the accessory chromos…
Comment: Genome Assembly QC from BAM files by SomeOne ▴ 240
There are some reference assemblies. Some close ones are at chromosome level but exact reference are not chromosome level assemblies. Othe…
Comment: Understanding the relationship between hhr and a3m output of HHblits by Joe 22k
Nice detective work! :)
Comment: Hifiasm is getting killed while trying to assemble a genome by pranavdatar01 • 0
The SRA accession is SRX12366993
Comment: SNP calling with bacterial assembled genome by GenoMax 153k
> After I find some differences between the assembly and the reference, how can I decide confident variants without the depth? Don't think…
Comment: Orthofinder Not Mapping to Any Orthogroups by Philipp Bayer 8.9k
Did you check whether your species' fasta file is named correctly? From memory Orthofinder will pull in files ending in .fa and .fasta in t…
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