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121,990 results • Page 647 of 2440
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5
votes
3
replies
3.8k
views
Flagstats and multiqc
multiqc samtools flagstat
updated 4.4 years ago by ★ 1.5k • written 4.4 years ago by • 0
0
votes
1
reply
1.6k
views
Does STAR index needs to be regenerated if I change program version?
rna-seq STAR
updated 4.4 years ago by 89k • written 4.4 years ago by ▴ 50
1
vote
0
replies
603
views
What does the GT(genotype) 0/0 means in final SV vcf file generated by SVABA?
genotype variation sv SVABA structral
4.4 years ago by Caronkey ▴ 10
0
votes
2
replies
726
views
blastn returns multiple identical lines
blast blastn
4.4 years ago by langziv ▴ 70
0
votes
2
replies
768
views
BGCs of angucyclines
BGCs
4.4 years ago by Rima ▴ 20
0
votes
1
reply
4.5k
views
Coxph Model Error: NA/NaN/Inf in foreign function call (arg 6)
r coxph survival
4.4 years ago by jack.henry ▴ 50
0
votes
0
replies
547
views
Comparasion of distributions
virus distributions estatistics genome
4.4 years ago by Carla • 0
1
vote
1
reply
719
views
Flooring (adjusting) values in Gene Expression Microarray data analysis?
gene-expression microarray R
updated 4.4 years ago by 89k • written 4.4 years ago by ▴ 270
0
votes
0
replies
522
views
how to assign novel multilocus sequence type
microbioloy
4.4 years ago by zhangdengwei ▴ 210
2
votes
4
replies
1.7k
views
paired-end fastq corruption cleanup: intersect of record headers in SeqIO.parse() iterators
ngs seqio sequencing alignment
updated 4.3 years ago by 154k • written 4.4 years ago by • 0
0
votes
4
replies
2.0k
views
Genepop for LD testing SNPs dataset
linkage genepop SNPs
updated 4.4 years ago by 11k • written 4.4 years ago by ▴ 30
1
vote
4
replies
2.1k
views
What's going on with my sleuth output?
RNA-seq Sleuth
4.4 years ago by a.sugi30 • 0
1
vote
5
replies
1.9k
views
RNA-seq of human cells and bacteria
Bacteria RNA-seq Human
updated 4.4 years ago by 89k • written 4.4 years ago by ▴ 50
3
votes
1
reply
798
views
how to find Gene ontology
GO
updated 4.4 years ago by ★ 19k • written 4.4 years ago by • 0
0
votes
2
replies
1.6k
views
Transfer annotation from fasta headers to associated gff
gff annotation fasta genome
updated 4.4 years ago by 9.3k • written 4.4 years ago by • 0
2
votes
3
replies
1.3k
views
velvet adjust MAXKMERLEGNTH on HPC
velvetoptimiser Velvet HPC
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 20
2
votes
4
replies
3.0k
views
PROKKA annotation problem - wrong reference?
prokka annotation
4.4 years ago by blur ▴ 280
3
votes
5
replies
1.7k
views
Nanopore sequencing of labelled DNA
sequencing nanopore
4.4 years ago by Jean-Karim Heriche 27k
0
votes
4
replies
1.8k
views
how to download dataset from NCBI dataset in python
python ncbi geodataset
4.4 years ago by salvatore.raieli2 ▴ 90
2
votes
12
replies
2.6k
views
How do I check the expression level of a unannotated lncRNA in RNAseq dataset?
LncRNAseq
updated 4.2 years ago by • 0 • written 4.4 years ago by • 0
0
votes
4
replies
4.2k
views
Maker Failed while doing repeat masking
maker annotation RepBase RepeatMasker
updated 4.4 years ago by 9.3k • written 5.5 years ago by ▴ 90
0
votes
15
replies
2.9k
views
compare two NCBI ftp tables
table NCBI
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 20
0
votes
0
replies
582
views
Differences between gene expression expressed as z-score or log2 values in Allen Brain Atlas
log2 expression allenatlas z-score
4.4 years ago by c.nunez • 0
2
votes
4
replies
1.4k
views
STAR after reverse complement with python
biopython STAR
4.4 years ago by lahavt • 0
1
vote
2
replies
1.3k
views
Heatmap from the coverage
transposons
4.4 years ago by bioinformatics.queries ▴ 70
0
votes
0
replies
675
views
Distinction of two very close bacterial strains
mutations bacteria
updated 2.0 years ago by 45k • written 4.4 years ago by ▴ 170
4
votes
1
reply
1.8k
views
Cellranger alignment options / parameters
Cellranger Alignment
updated 4.4 years ago by ★ 19k • written 4.4 years ago by ▴ 70
0
votes
0
replies
550
views
SNPsnap
SNPsnap
4.4 years ago by Niamh • 0
0
votes
7
replies
3.4k
views
Changing sample name in multiple VCF files
gatk bcftools linux vcf
updated 4.4 years ago by 89k • written 4.4 years ago by • 0
0
votes
0
replies
2.0k
views
Suggestions for doing differential expression with 10x single cell data (two conditions, 4 replicates each, having 30K cells in each conditions))
edgeR rnaseq singlecellrnaseq deseq2 seurat
4.4 years ago by m.sadman.sakib ▴ 120
3
votes
22
replies
4.4k
views
R Programming for Differential Gene Expression Analysis
Ballgown RNA-SEQ Programming R DEG
4.4 years ago by HaroonPakistan • 0
7
votes
9
replies
12k
views
8 follow
Any methods available to do QC analysis of Pacbio raw data??
Assembly genome Pacbio next-gen sequencing
updated 2.5 years ago by • 0 • written 8.0 years ago by ▴ 130
4
votes
3
replies
3.8k
views
narrowPeak or summits.bed for HOMER motif finding
motif motiffinding homer macs bedformat
updated 4.4 years ago by ★ 1.7k • written 4.4 years ago by ▴ 130
0
votes
1
reply
825
views
Obtain identity of sequences aligned by msa in r
r msa clustalw
updated 4.4 years ago by 21k • written 4.4 years ago by • 0
4
votes
2
replies
3.3k
views
Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle5.0 beagle
updated 2.6 years ago by 45k • written 6.3 years ago by ★ 9.6k
2
votes
2
replies
2.2k
views
Google Cloud for RNA seq analysis
googlecloud gcp RNAseq Cloud
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 270
0
votes
4
replies
1.1k
views
Viral Genome reconstruction
lectures genome virus sequencing matches
4.4 years ago by Carla • 0
0
votes
2
replies
1.7k
views
How can I retrieve genomic sequences from ENSEMBL in a window both up stream and downstream of the TSS?
sequence Genome ensembl motif
updated 4.4 years ago by 24k • written 4.4 years ago by • 0
2
votes
14
replies
4.4k
views
Extract information from Ensembl
SNP automation python Ensembl
updated 4.4 years ago by 56k • written 4.4 years ago by • 0
2
votes
4
replies
5.0k
views
bcftools multiple commands
bcftools
4.4 years ago by Filago ▴ 110
1
vote
1
reply
2.7k
views
what pihat cutoffs from plink --genome are 3rd degree relative
related ibd plink
4.4 years ago by curious ▴ 900
0
votes
3
replies
1.1k
views
Statistical distribution of viral genomes
genome virus statistics gauss distribution
updated 4.4 years ago by 56k • written 4.4 years ago by • 0
0
votes
0
replies
838
views
News: New workshops from UC Davis Bioinformatics Core
workshop
4.4 years ago by najoshi ▴ 30
6
votes
2
replies
1.0k
views
How to create a new column with for and if/else
R
updated 2.3 years ago by 45k • written 4.4 years ago by ▴ 20
0
votes
3
replies
1.8k
views
ENCODE: Why are there more than one bed narrowPeak file for each DNase-seq experiment (but only one bed file accession is given in the download list)?
narrowPeak ENCODE bed accession
4.3 years ago by edostyles • 0
0
votes
0
replies
543
views
How to make a skyline plot from ddRAD data
ddRAD skyline BEAST
4.4 years ago by mesembriomys • 0
1
vote
1
reply
850
views
PDB editing using BASH (Linux)
Renumbering awk BASH PDB
updated 4.4 years ago by ★ 30k • written 4.4 years ago by • 0
4
votes
3
replies
2.0k
views
Forum: Given my background, what are my chances of being accepted into a PhD program at Harvard/MIT?
mit PhD gradschool admission harvard
updated 4.1 years ago by 45k • written 4.4 years ago by • 0
0
votes
1
reply
962
views
RNA_Seq data aligned used uniquely or multi mapped reads impact on result interpretation
NGS Transcriptomic GENOMIC
updated 4.4 years ago by 154k • written 4.4 years ago by • 0
0
votes
3
replies
5.0k
views
Please help with the famous 00LOCK error in r
R
updated 4.4 years ago by 56k • written 4.7 years ago by ▴ 30
121,990 results • Page 647 of 2440
Recent Votes
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
Comment: Quantification using salmon in alignment-based mode after minimap2 run
Answer: Quantification using salmon in alignment-based mode after minimap2 run
Comment: Quantification using salmon in alignment-based mode after minimap2 run
Answer: Corresponding BAM files
Answer: Tools To Calculate Average Coverage For A Bam File?
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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…
Answer: ::Last Call:: In-Person Workshop - NGS Epigenomics Data Analysis (November 3-5 i by ecSeq Bioinformatics ▴ 20
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…
Answer: Best set of tools / workflows for predicting the biosynthesis pathways of comple by ehaag ▴ 100
I tried [searching for tools in the NIAID Data Ecosystem][1] and found something that may be relevant. [PathPred][2] is an enzyme catalyzed…
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere by ehaag ▴ 100
I did a quick [search for tools in the NIAID Data Ecosystem][1] and found a few that map Illumina short reads onto a reference genome, incl…
Answer: Corresponding BAM files by GenoMax 154k
You can get BAM files for 10x single-cell data and they can be found under the `Data Access` tab of the SRA record under the `Original Form…
Comment: GTF file for HIV strain pNL4-3 by Ales ▴ 50
All of the genome assemblies are from the LANL compendiu, match accession with GENBANK (>2,000 complete genome assemblies from the 2021 LAN…
Comment: Hisat2 splice sites extract blank files by Ales ▴ 50
hisat2_extract...py scripts make several assumptions about the input GTF files. For example, they require gene_id field to be present for a…
Comment: GTF file for HIV strain pNL4-3 by GenoMax 154k
> This project started from my personal need to improve spliced alignment Are there plans to submit these annotations to NCBI/EBI? Are yo…
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