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121,819 results • Page 421 of 2437
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4
replies
1.4k
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admixture mem error, but not out of RAM
admixture
3.3 years ago by dec986 ▴ 380
0
votes
0
replies
889
views
IGV Sashimi plot from ONT long read sequencing of cDNA amplicons
splicing oxford long-read sashimi nanopore
updated 3.3 years ago by 153k • written 3.3 years ago by • 0
6
votes
3
replies
2.7k
views
How to download a large number of protein.faa.gz files from NCBI's FTP site in one go
NCBI entrez FTP efetch
3.3 years ago by beginner123 ▴ 30
0
votes
0
replies
563
views
Filtering metagenome amplicon sequencing data
data metagenome QIIME2
3.3 years ago by kocharovskayaj • 0
0
votes
1
reply
698
views
Chromosomal location not matching the mRNA sequence
transcription NCBI mutation Variant ClinVar
updated 3.3 years ago by 103k • written 3.3 years ago by • 0
0
votes
7
replies
4.3k
views
RNA-seq QC - adapter content and high duplication
RNA-seq Control FASTQC Quality
updated 3.3 years ago by 153k • written 3.3 years ago by ▴ 10
0
votes
0
replies
355
views
K means clustering of expression data of different bacterial species using orthologous groups
clustering
3.3 years ago by Thomas • 0
1
vote
3
replies
4.3k
views
Forum: What counts as a valid biological replicate in single cell RNAseq?
statistics biological replicates scRNA-seq
updated 3.3 years ago by 4.1k • written 3.3 years ago by • 0
3
votes
5
replies
1.9k
views
Biopython - How to break down lineage from either nucleotide db or taxonomy db?
python genbank biopython
updated 3.3 years ago by 103k • written 3.3 years ago by ▴ 20
11
votes
5
replies
2.5k
views
Rename part of file name using a two column csv/tsv
rename bash
updated 3.3 years ago by 8.7k • written 3.3 years ago by • 0
5
votes
7
replies
2.6k
views
how to retrieve protein.fasta from genome in NCBI
NCBI
3.3 years ago by beginner123 ▴ 30
0
votes
2
replies
1.2k
views
Gene Ontology and Pseudotime analysis in scRNA-seq
GO pseudotime
3.3 years ago by Basti ★ 2.1k
2
votes
2
replies
3.2k
views
How to interpret two letter codes of COG category obtained from EggNOG tool?
Assembly genome proteins genes
updated 2.7 years ago by 45k • written 3.3 years ago by ▴ 120
27
votes
5
replies
2.7k
views
6 follow
Tool: Efficient querying of genomic reference databases with gget
ensembl enrichr ncbi gget uniprot
updated 3.3 years ago by ▴ 720 • written 3.3 years ago by ▴ 450
1
vote
3
replies
2.0k
views
Bioinformatics with python Cookbook 2nd edition issues
docker token issues
3.2 years ago by Raz • 0
1
vote
6
replies
1.7k
views
Comparative transcriptomics
rna-seq comparative transcriptomics
updated 2.3 years ago by 4.8k • written 3.3 years ago by ▴ 60
1
vote
4
replies
2.2k
views
using vcffilter
vcffilter vcftools
updated 3.3 years ago by ▴ 90 • written 3.3 years ago by • 0
2
votes
1
reply
975
views
somatic SNV tool for ONT samples
somatic ont SNV
updated 3.3 years ago by 4.8k • written 3.3 years ago by ▴ 10
1
vote
3
replies
1.4k
views
R package plyr：count output int not num
R
updated 3.3 years ago by 28k • written 3.3 years ago by • 0
3
votes
4
replies
3.3k
views
I don't understand the HDF5 file from 10x genomics scRNAseq
10x hdf5
15 months ago by jonas.andersson ▴ 40
3
votes
2
replies
1.5k
views
What's the best 3rd party software for doing analysis on 10X Genomics ATAC-seq data?
atac-seq 10X
updated 3.3 years ago by ▴ 800 • written 6.3 years ago by ▴ 200
0
votes
0
replies
511
views
custom sizing question in ggseqlogo. sequence logo creation
logo sequence R ggseqlogo
3.3 years ago by RNAseqer ▴ 280
2
votes
1
reply
728
views
How do I identify cells containing a Transgene in my 10x Chromium scRNAseq data
10x Transgene scRNAseq Genomics
updated 3.3 years ago by 89k • written 3.3 years ago by ▴ 10
3
votes
8
replies
2.0k
views
Error while running blastn
blastn
updated 3.3 years ago by 45k • written 3.3 years ago by ▴ 10
0
votes
1
reply
927
views
GATK MQ-scores differ depending on reference genome
gatk filtration variant vcf
updated 3.3 years ago by ▴ 160 • written 3.3 years ago by ▴ 10
1
vote
1
reply
1.3k
views
bedtools getfasta duplicated fasta
fastaFromBed duplicates getfasta
updated 3.3 years ago by 9.3k • written 3.3 years ago by ▴ 30
0
votes
2
replies
728
views
Biomarker analysis from TCGA cancer data
Biomarker TCGA
3.3 years ago by radhuladani62 • 0
1
vote
2
replies
1.8k
views
Limma voom with missing values from mass spectrometry
differential protein missing t-test. Limma
updated 3.3 years ago by ★ 8.3k • written 3.3 years ago by ▴ 20
0
votes
0
replies
402
views
Transcriptomics nrichment analysis of M. acuminata comparing gene IDs with model plant organisms
Model Transcriptomics Musa Enrichment
3.3 years ago by melcrive • 0
0
votes
0
replies
581
views
What does it mean by a "site" in the case of a CG model?
coarse-grained modeling simulation
3.3 years ago by user366312 ▴ 20
3
votes
2
replies
966
views
Filter Protein Expression Data
Filtering Proteomics
updated 3.3 years ago by 45k • written 3.3 years ago by ▴ 170
2
votes
2
replies
2.4k
views
Count number of unique cell barcode (CB) in bam file
cell-ranger samtools BAM cell-barcode
updated 2.2 years ago by 45k • written 3.3 years ago by ▴ 40
2
votes
2
replies
1.4k
views
Where is EBV decoy sequence in the Cellranger GRCh38 reference genome?
cellranger reference grch38 genome decoy
3.3 years ago by lh0101 • 0
0
votes
2
replies
961
views
Mobile element discovery with MELT brings different results when chromosomes are analysed separate
melt
3.3 years ago by optimistsso4co3 ▴ 140
3
votes
1
reply
695
views
Delete individuals
dogs GWAS
updated 3.3 years ago by 11k • written 3.3 years ago by • 0
2
votes
2
replies
1.3k
views
RT-PCR primer design
RT-PCR
3.3 years ago by Fatemeh Nabizadeh ▴ 10
5
votes
4
replies
2.0k
views
Primer designing for full length gene amplification
gene-amplification primer-design offtopic
updated 23 months ago by 45k • written 3.3 years ago by ▴ 30
0
votes
0
replies
1.4k
views
Job: Bioinformatics Analyst - University of Minnesota Genomics Center
position
3.3 years ago by jgarbe ▴ 10
0
votes
0
replies
720
views
How to extract promoter coordinates from transcriptome.gtf file generated after cuffmerge ? file only has exon in annotation
cuffmerge promoter
updated 13 months ago by 45k • written 3.3 years ago by ▴ 10
1
vote
2
replies
1.3k
views
PLINK and PLINK2, AF and MAF
maf plink af vcf
3.3 years ago by Sammy ▴ 30
0
votes
1
reply
751
views
Consensus taxonomic annotation BLAST - NCBI_nr
NCBI BLAST taxonomy annotation metagenomes
updated 3.3 years ago by 153k • written 3.3 years ago by ▴ 60
0
votes
1
reply
884
views
Auto dock
Drug design
updated 3.3 years ago by ★ 29k • written 3.3 years ago by • 0
6
votes
13
replies
2.5k
views
Best configuration workstation for our lab
ion workstation S5 NIPT torrent NGS
updated 3.3 years ago by 56k • written 3.3 years ago by • 0
0
votes
0
replies
519
views
Parametric proportional hazards model based on the Gompertz distribution
distribution Gompertz Survival analysis
3.3 years ago by Yong ▴ 10
0
votes
6
replies
1.7k
views
VCFtools error
vcf vcftools
3.1 years ago by Sammy ▴ 30
5
votes
2
replies
962
views
trim fasta header, remove after hash (#)
header fasta hash trim
updated 3.3 years ago by 21k • written 3.3 years ago by ▴ 80
3
votes
3
replies
1.5k
views
Forum: Looking for a PostDoc position in ML-heavy medical bioinformatics in Germany
Germany PostDoc
updated 3.3 years ago by 27k • written 3.3 years ago by ★ 3.0k
2
votes
2
replies
1.3k
views
Could bowtie2 use a fasta file as input to be mapped against a reference genome?
BAM bowtie2
updated 2.5 years ago by 45k • written 3.3 years ago by • 0
3
votes
2
replies
1.0k
views
Tree shape uploaded on iTOL is different from trees constructed by another tools.
dendrogram iTOL phylogram
updated 3.3 years ago by 56k • written 3.3 years ago by • 0
0
votes
2
replies
1.9k
views
LEfSe - Issue when plotting using the python script plot_res.py (Traceback (most recent call last)
metadata differentially taxa lefse abundant qiime2 numerical-categorical
updated 3.3 years ago by 3.9k • written 4.2 years ago by • 0
121,819 results • Page 421 of 2437
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Recent Replies
Comment: Add reference genomes as an outgroup to a phylogenetic tree by Michael 56k
That's interesting from a Norwegian perspective. You also may find [SalmoBase][1] useful. [1]: https://salmobase.org/#About
Comment: deeparg-takes-too-many-threads by Dave Carlson ★ 2.1k
I'm not particularly familiar with Concoct, but from glancing [at the code][1], it does appear to use OpenMP, so I would expect that setti…
Comment: Learning Bioinformatics doing Projects by Pierre Lindenbaum 166k
This post does not fit the theme of this forum.
Comment: Learning Bioinformatics doing Projects by jared.andrews07 ★ 19k
There is nothing stopping you from doing those things. This is not a question.
Comment: deeparg-takes-too-many-threads by GenoMax 153k
Related past thread for reference: https://www.biostars.org/p/9613794/ , in case you know about the programs mentioned.
Comment: best practice for diploid variant calling by cmdcolin ★ 4.3k
that is quite a cool experiment. I am not actually sure of the best approach (sorry to disappoint). I think that if you look up "phased ass…
Comment: Add reference genomes as an outgroup to a phylogenetic tree by dthorbur ★ 3.1k
I'm sure there are phylogenetics papers out there comparing species within this genus - a quick google seems to suggest there is up to 15M …
Comment: deeparg-takes-too-many-threads by Dave Carlson ★ 2.1k
Note that vsearch uses pthreads, *not* OpenMP, for multithreading. Therefore setting OpenMP environment variables (e.g., `OMP_NUM_THREADS`…
Comment: Add reference genomes as an outgroup to a phylogenetic tree by Álvaro • 0
Thank you I will try this!
Comment: Add reference genomes as an outgroup to a phylogenetic tree by Álvaro • 0
I'm working with Salmo trutta and wanted to use Salmo salar as an outgroup. I have whole-genome .fastq data of the trout samples. Sorry, I'…
Comment: deeparg-takes-too-many-threads by GenoMax 153k
> I am running it withing a screen session If you are using `screen` then you may need to set the variables in a different way. Try to se…
Comment: deeparg-takes-too-many-threads by shevch2009 ▴ 20
Thanks, I will look for another tools. Yes, I am running it withing a screen session.
Comment: deeparg-takes-too-many-threads by GenoMax 153k
If the program is not respecting limits you are setting then you may need to dive into code to see why that is happening. It may or may not…
Comment: When to merge RNA-seq files with multiple sequencing lanes by GenoMax 153k
> how I should combine the files together and at what point? Samples running in multiple lanes represent technical sequencing replicates a…
Comment: Low percentage of classified reads (~18%) after Kraken2 analysis – is this expec by GenoMax 153k
To note: files in https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA directory are over a year old at this point. They are no longer being made a…
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