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121,896 results • Page 6 of 2438
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1
vote
2
replies
527
views
Seurat DimPlot generates a weird data frame together with the scatter plot
R Seurat
6 weeks ago by solo.albif • 0
5
votes
5
replies
5.2k
views
How to download intronic positions from Ensembl
genome ensembl
updated 6 weeks ago by • 0 • written 9.6 years ago by ▴ 50
0
votes
11
replies
860
views
Current size of blast nr database as FASTA file
fasta blast
updated 6 weeks ago by 15k • written 6 weeks ago by • 0
1
vote
5
replies
690
views
SRA FTP Upload Issue
FTP SRA NCBI
updated 6 weeks ago by ▴ 880 • written 6 weeks ago by ▴ 10
4
votes
4
replies
578
views
How to calculate total and average read counts from paired-end and singleton FASTQ files?
Metagenomics
updated 5 weeks ago by 153k • written 6 weeks ago by ▴ 20
2
votes
1
reply
405
views
New computer purchase
Linux
updated 6 weeks ago by 153k • written 6 weeks ago by • 0
0
votes
0
replies
697
views
News: Python for Biological Data Exploration & Visualization (PYBD01)
Python
updated 6 weeks ago by 153k • written 6 weeks ago by ▴ 110
0
votes
0
replies
647
views
News: Introduction to Machine Learning (IMLR04)
Learning R Machine
updated 6 weeks ago by 153k • written 6 weeks ago by ▴ 110
0
votes
2
replies
536
views
When absolute protein quantification isn't possible, what anaylses work on ranked expression?
DIA-MS proteomics
updated 5 weeks ago by 45k • written 6 weeks ago by • 0
0
votes
0
replies
396
views
lncRNA and mRNA correlation analysis results
correlation lncRNA ncRNA coexpression mRNA
6 weeks ago by Zeynep • 0
0
votes
2
replies
804
views
Scanpy Dotplot / Matplotlib Help
Matplotlib Dotplot Python Scanpy
6 weeks ago by cthangav ▴ 110
0
votes
0
replies
392
views
TOPMed Imputation - More than 10000 allele switches
imputation topmed
6 weeks ago by Akshaj • 0
4
votes
2
replies
520
views
Help regarding quality control of 10X run?
10x nuclei qc scnuc
updated 6 weeks ago by ★ 19k • written 6 weeks ago by ★ 1.1k
0
votes
1
reply
483
views
PLINK 1.9 and ADMIXTURE 1.3.0 Help with renaming
Admixture error Plink debugging coding
updated 6 weeks ago by ▴ 660 • written 6 weeks ago by • 0
0
votes
0
replies
360
views
salmon alevin multimapping reads/ tier3 genes
salmon alevin
6 weeks ago by nmannda148 • 0
5
votes
3
replies
553
views
How can I confidently determine if my genome sequence Is truly Anaplasma marginale?
anaplasma genomics marginale omics
updated 5 weeks ago by 45k • written 6 weeks ago by • 0
3
votes
11
replies
1.0k
views
Trouble with Standalone Blast Tool (running for 2 hours and no output)
genome fasta blastx blast
updated 6 weeks ago by ★ 30k • written 6 weeks ago by • 0
0
votes
0
replies
503
views
Seeking unique bioinformatics angle for wildlife-livestock AMR gut microbiome study (PhD proposal help)
microbiome amr bioinformatics metagenomics antimicrobial-resistance
6 weeks ago by Saeed • 0
0
votes
0
replies
349
views
MDS file NaN values
missing genome MDS
6 weeks ago by am29 ▴ 60
0
votes
6
replies
748
views
Running Arriba on galaxy
Galaxy
6 weeks ago by Abdelrahman • 0
2
votes
4
replies
576
views
how to extract centromeric regions from human assemblies/FASTA
centromeres FASTA
updated 6 weeks ago by 7.9k • written 6 weeks ago by ▴ 130
0
votes
1
reply
479
views
Changes cgMLST type of Neisseria gonorrhoeae
cgMLST Neisseria gonorrhoeae
updated 6 weeks ago by 153k • written 6 weeks ago by • 0
0
votes
0
replies
344
views
Appropiate normalization method for OTU table built from MAGs abundances estimations?
MAG normalization OTUs metagenomics
6 weeks ago by v.berriosfarias ▴ 140
0
votes
1
reply
423
views
scRNA-seq annotation with Revsc
epithelialcells intestinal Revivalstemcell
updated 6 weeks ago by 3.4k • written 6 weeks ago by • 0
1
vote
3
replies
564
views
dbSNP: left-shift vs right-shift of indels
dbSNP
updated 6 weeks ago by 153k • written 7 weeks ago by ▴ 10
1
vote
3
replies
516
views
duplicate reads in RNAseq datasets
RNAseq R
updated 6 weeks ago by ★ 7.7k • written 6 weeks ago by ▴ 470
0
votes
0
replies
292
views
TOM matrix WGCNA
WGCNA
6 weeks ago by frarodmar17 • 0
0
votes
0
replies
515
views
Tools to model DEG/pathways in (fast-dividing) CANCER cell lines across timepoints? (in bulk RNA-seq)
DEG RNA-seq bulk
6 weeks ago by txema.heredia ▴ 250
8
votes
5
replies
6.8k
views
Combine a directory of GVCF files with gatk CombineGVCFs
gatk combinegvcfs gvcf
updated 6 weeks ago by ★ 4.4k • written 3.8 years ago by ▴ 210
0
votes
4
replies
611
views
UMI introduction and deduplication with SMARTer-Seq
RNAseq sequencing UMI RNA
updated 6 weeks ago by 22k • written 7 weeks ago by • 0
0
votes
0
replies
648
views
News: AI for Genomics: From CNNs and LSTMs to Transformers (Online, 9–11 September)
DeepLearning LSTMs AI CNNs MachineLearning
7 weeks ago by Physalia-courses ★ 2.6k
1
vote
1
reply
450
views
AMRFinderPlus input fasta file for clinical isolates
AMRFinder
updated 7 weeks ago by 153k • written 7 weeks ago by • 0
0
votes
1
reply
395
views
Merged seurat objects, clustering problem, help please
harmony seurat clustering scRNA
updated 7 weeks ago by 89k • written 7 weeks ago by • 0
0
votes
4
replies
593
views
Linkage disequilibrium estimation in unphased data?
correlation WES Pearson LD Kendall
6 weeks ago by Joel Wallenius ▴ 220
2
votes
6
replies
733
views
Why do Sox9 and Amh, which are Sertoli cell markers, show expression in the overall cell population?
analysis scRNA-seq
6 weeks ago by Bio • 0
0
votes
1
reply
416
views
ONT bulk PCR cDNA protocol
bulk ONT PCR adapter UMI
updated 7 weeks ago by 153k • written 7 weeks ago by • 0
8
votes
7
replies
1.8k
views
6 follow
Fungal Annotation Comparison
Annotation RNAseq Fungus genome_assembly funannotate
updated 7 weeks ago by ▴ 70 • written 3 months ago by ▴ 240
1
vote
3
replies
510
views
VCF Header malformation
update Vcf dictionary mismache header
updated 7 weeks ago by 23k • written 7 weeks ago by ▴ 20
0
votes
0
replies
640
views
News: Unlock the Power of Python for Biological Research: PYBD01
Python
updated 7 weeks ago by 153k • written 7 weeks ago by ▴ 110
0
votes
6
replies
865
views
STAR alignment to small fasta file failing
seq STAR alignment RNA
7 weeks ago by campbio • 0
0
votes
0
replies
707
views
Job: Postdoctoral Researcher (DFG‑funded): AI & Ageing Biology
bioinformatics longevity aging AI open-source
7 weeks ago by Anton ▴ 100
1
vote
3
replies
564
views
ONT Methylation calling
MODIFICATIONS NANOPORE ONT EPIGENETIC SEQUENCING
updated 6 weeks ago by 7.9k • written 7 weeks ago by • 0
1
vote
3
replies
918
views
picard MarkDuplicates READ_PAIRS_EXAMINED much lower than the number of read pairs successfully mapped by STAR
STAR removal RNA-seq picard duplicate
updated 6 weeks ago by 153k • written 7 weeks ago by • 0
1
vote
6
replies
3.2k
views
Which threshold to be put in the MAPQ when doing mpileup of BCF tools on a STAR-generated BAM file ?
RNAseq STAR
updated 7 weeks ago by ▴ 910 • written 2.8 years ago by ▴ 30
1
vote
1
reply
642
views
Mendelian Randomization, Liftover
Mendelian-Randomization Liftover Genetics
updated 7 weeks ago by • 0 • written 11 months ago by ▴ 10
3
votes
4
replies
663
views
Identifying primers in rna-seq data
cutadapt transcriptomics fastqc rna-seq primers
updated 7 weeks ago by 89k • written 7 weeks ago by • 0
0
votes
6
replies
695
views
Plant transcriptome analysis and annotation
plants sRNA-Seq adnnotation analysis expression
7 weeks ago by martta95 ▴ 10
1
vote
1
reply
416
views
Is Dorado, nanopolish, and xpore compatible with each other?
nanopolish ONT Dorado samtools xPore
updated 7 weeks ago by 153k • written 7 weeks ago by • 0
1
vote
2
replies
510
views
Average Nucleotide Identity for bins
ANI bin data shotgun
7 weeks ago by shevch2009 ▴ 20
0
votes
0
replies
581
views
News: Introduction to Python for Biologists (IPYB01)
Python
updated 7 weeks ago by 153k • written 7 weeks ago by ▴ 110
121,896 results • Page 6 of 2438
Recent Votes
Answer: Structural Variant identification on pangenome graphs
Multiple VCF file comparision
Comment: Different UMAP for batch correction in R and Pytho
Answer: Is a direct comparison of the number of up- and down-regulated genes meaningful?
allele frequency in VCF
Comment: Best way to do protein structure guided similarity search?
Comment: Tool 'sra_source' does not exist.
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Comment: Transfer harmony-integrated scRNA-seq data to scanpy by Madiha ▴ 10
Hi, I am not sure if you still remmeber the solution you followed that time. But I am stuck with similar problem. scVI is not working good …
Answer: Pipeline for downloading, aligning, and curating influenza A and B sequences for by GenoMax 153k
Have you looked at https://nextstrain.org/ and specifically https://github.com/nextstrain/seasonal-flu Software is available to do the ana…
Comment: Different UMAP for batch correction in R and Pytho by GenoMax 153k
Use this tutorial for how to upload images: https://www.biostars.org/p/309884/#346553 Only difference is instead of using an external imag…
Answer: GTEx sQTL v8 – annotation version used? by GenoMax 153k
If you click over to the `Reference` tab ( https://gtexportal.org/home/downloads/adult-gtex/reference ), it looks like they used GENCODE v.…
Comment: How to Identify Conserved 21-mers Across TE Insertions in Drosophila? by manikin_python9f ▴ 20
Since they are transposons, we don’t know the exact location of them. We know their sequence of insertions from repeatmasker in dm6 genome.…
Comment: Tool 'sra_source' does not exist. by Atefeh • 0
Thanks for your kindness.
Comment: TCGA -derived Large RangeSummarizeExperient file by Tom • 0
It works well. Thank you very much ! @atpoint
Answer: TCGA -derived Large RangeSummarizeExperient file by ATpoint 89k
For the end user these `DFrames` are just regular data.frames, so you can do `col_data[,c("barcode", "patient", "whatever")]` or just do `a…
Comment: magpurify errors by shevch2009 ▴ 20
I have checked with my eyes, and I didn't find it, I have only one contig that starts with k127_458 .... but the name is different - k127_4…
Comment: Yeast reference-based genome assembly by Michael 56k
So, you aren't sure about the exact species? Then you might want to be careful with reference-based assembly in general. I recommend the fo…
Comment: Structural Variant identification on pangenome graphs by Panos ★ 1.8k
That's a very comprehensive list! Thanks for sharing! `minigraph` better suits my needs because all I need is SVs for my genomes. As far a…
Comment: Yeast reference-based genome assembly by amy967107 • 0
I have ~2.01 Gb of ONT data and the target genome is ~20–23 Mb (90–100× coverage). My ONT read N50 is ~3.8 kb, so contiguity may be limited…
Comment: Yeast reference-based genome assembly by amy967107 • 0
This is a yeast strain (probably Rhodotorula spp.) and I'm trying to assemble the entire genome from nanopore reads using a reference-based…
Answer: Yeast reference-based genome assembly by Michael 56k
The new [hifiassm ONT][1] may be all you need for getting a good assembly. I would not recommend LRSDAY, except for its annotation part (wh…
Comment: magpurify errors by Mensur Dlakic ★ 30k
By the way, these errors are not unique. If you look through the `magpurify` GitHub issues, both types have been reported already. - https…
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