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3
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0
replies
1.3k
views
Herald: The Biostar Herald for Thursday, May 11, 2023
herald
2.4 years ago by Biostar 3.6k
0
votes
4
replies
1.5k
views
csv to custom manifest file
illumina
2.4 years ago by bioguy24 ▴ 230
13
votes
14
replies
4.2k
views
Pan genome based assembly
denovo ngs
updated 2.3 years ago by 4.8k • written 2.4 years ago by ▴ 10
6
votes
2
replies
1.2k
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq sequency_depth sequencer library_size multiplexing
updated 2.4 years ago by 154k • written 2.4 years ago by ▴ 20
3
votes
2
replies
1.4k
views
Is the gene-specific PCR efficiency a serious concern for intrasample comparisons in RNA-Seq?
RNA-Seq normalization bias PCR_efficiency intrasample_comparison
updated 2.4 years ago by 4.2k • written 2.4 years ago by ▴ 20
0
votes
0
replies
581
views
Create bed file where each column is the number of intersections with another bed file
bedtools
updated 2.3 years ago by 45k • written 2.4 years ago by • 0
4
votes
3
replies
2.4k
views
Ncbi protein id mapping to uniprot id
Proteomics
2.4 years ago by samueldelacamara • 0
0
votes
0
replies
536
views
XCMS library not centroid mode
xcms R
2.4 years ago by t.ru ▴ 20
6
votes
6
replies
8.0k
views
6 follow
How To Retrieve Data From Jgi Automatically Given A Set Of Ids?
r python api xml
updated 2.4 years ago by 154k • written 11.9 years ago by 4.1k
1
vote
4
replies
6.7k
views
active.ident slot present but not recognized in seurat object
Seurat Idents
updated 2.4 years ago by ★ 1.9k • written 2.4 years ago by • 0
0
votes
4
replies
1.1k
views
Detect mutations in clonally propagated plants
mutations Illumina clonal-propagation variant-calling
2.4 years ago by RvV ▴ 30
0
votes
0
replies
493
views
PheWAS - risk/effect allele
GWAS PheWAS Open_Targets_Genetics
2.4 years ago by MH85 ▴ 20
3
votes
9
replies
3.8k
views
Finding TF motifs enriched in series of ATAC-seq peaks (using fimo?)
MEME ATAC-Seq TF FIMO motif
2.4 years ago by octopuslegs11 ▴ 10
2
votes
1
reply
847
views
'Seurat' package
Seurat R
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 20
0
votes
1
reply
1.3k
views
How can I create more accurate admixture plot like this?
admixture vcf plink
updated 2.4 years ago by 45k • written 2.4 years ago by • 0
3
votes
3
replies
2.1k
views
News: NCBI's IgBLAST version 1.21.0 is now available
IgBLAST BLAST T-Cell NCBI receptors
2.4 years ago by PeterC_NCBI ▴ 520
1
vote
2
replies
983
views
`MOFAobject@expectations` is empty list
MOFA2
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 180
1
vote
5
replies
1.8k
views
How to get uniprot accessions from a multi protein sequence fasta file
uniprotkb uniprot proteomics
updated 2.4 years ago by 154k • written 2.4 years ago by ▴ 20
5
votes
5
replies
1.5k
views
Normalizing RNA read counts for each gene?
normalization RNA-seq metatranscriptomes
updated 2.4 years ago by ★ 1.9k • written 2.4 years ago by ▴ 10
8
votes
6
replies
2.2k
views
No differentially expressed genes after multiple testing correction in mice
edgeR DESeq2 Limma mouse RNA-seq
updated 2.4 years ago by 11k • written 2.4 years ago by ▴ 40
0
votes
5
replies
2.1k
views
How to trim reads for Chip Seq analysis
base content sequence
updated 2.4 years ago by ▴ 220 • written 2.4 years ago by • 0
0
votes
2
replies
802
views
How to use trimmomatic to cut the final part of bases
BASE SEQUENCE CONTENT
updated 2.4 years ago by 45k • written 2.4 years ago by • 0
0
votes
1
reply
815
views
Can I perform ANOVA test on rlog data of RNA sequencing counts?
rlog ANOVA
updated 2.4 years ago by 3.9k • written 2.4 years ago by ▴ 180
3
votes
1
reply
1.3k
views
How do I use the new human pangenome reference to discover SNV and SV.
pangenome reference graph vg
2.4 years ago by Pierre Lindenbaum 166k
3
votes
4
replies
1.6k
views
remote tblastn database name(s)
blast database tblastn
updated 2.4 years ago by ★ 30k • written 2.4 years ago by ▴ 140
0
votes
0
replies
1.3k
views
Understanding the output from Eggnog mapper
inparanoid orthology eggnog
2.4 years ago by The ▴ 180
1
vote
2
replies
1.2k
views
What is the best aligner for stranded RNASeq
aligner stranded RNAseq
updated 2.4 years ago by 13k • written 2.4 years ago by ▴ 370
0
votes
4
replies
1.1k
views
To match fragments within range - Python or awk
awk python
2.4 years ago by L_bioinfo • 0
0
votes
2
replies
1.7k
views
manually calculate log2 fold change and compare
edgeR log2foldchange RNA-seq
updated 2.4 years ago by 89k • written 2.4 years ago by • 0
1
vote
4
replies
1.2k
views
My VCF file structure is strange and less compatible to data processing programs.
VCF GATK SNPs
updated 2.4 years ago by 103k • written 2.4 years ago by • 0
3
votes
4
replies
3.5k
views
Sub-sampling a BAM to a fixed number of reads
samtools BAM
updated 2.3 years ago by 45k • written 2.4 years ago by ▴ 10
0
votes
6
replies
4.8k
views
terminal can't activate base automatically (conda)
conda
updated 4 months ago by • 0 • written 4.1 years ago by ▴ 20
0
votes
1
reply
691
views
How to analyse scaffold assembly errors?
Scaffold
updated 2.4 years ago by 103k • written 2.4 years ago by • 0
1
vote
2
replies
919
views
Similarity search and strand difference
blat bwa-mem2
2.4 years ago by L_bioinfo • 0
8
votes
6
replies
3.7k
views
DESeq2 error while using apeglm - optimHess
optimHess Apeglm DESeq2
updated 2.4 years ago by 89k • written 2.5 years ago by ▴ 40
2
votes
1
reply
1.2k
views
Obtention of the binomial transformed count table with edgeR
RNA-Seq counts edgeR CPM DeSeq2
updated 2.4 years ago by 89k • written 2.4 years ago by • 0
0
votes
0
replies
604
views
News: course- Population genomic inference from low-coverage whole-genome sequencing data
Whole-Genome-Sequencing Population-Genomics
updated 2.4 years ago by 45k • written 2.4 years ago by ★ 2.6k
1
vote
2
replies
4.7k
views
SnpSift: Annotate vcf file using GNOMAD
GNOMAD SnpEff SnpSift
updated 2.4 years ago by 45k • written 4.5 years ago by ▴ 250
0
votes
0
replies
2.9k
views
from seurat to scanpy data conversion and re-scaling
transctiptome eurat scanpy conversion spatial
2.4 years ago by Omics data mining ▴ 260
0
votes
2
replies
1.5k
views
Gene Set Enrichment Analysis
GSEA Functional-analysis
2.4 years ago by ahmad • 0
1
vote
2
replies
1.5k
views
Problem while downloading SRA using aspera links
sra aspera fastq
14 months ago by chatterjeejayeeta100 • 0
0
votes
0
replies
469
views
download dataset of annotated gene and the domains it contains
domains database
2.4 years ago by pick • 0
1
vote
0
replies
502
views
mirdeep2- unable to extract files for mapping -extract_miRNAs: command not found error
miRNA miRDeep2 miRNAanalysis
2.4 years ago by Supernova • 0
0
votes
5
replies
2.0k
views
combine/merge closet variants into one from mutect2
variants mutect2 merge gatk
updated 2.4 years ago by 103k • written 2.4 years ago by ▴ 930
0
votes
1
reply
962
views
GDC API: Obtain the Objective Power (or Magnification) of a WSI file
GDC WSI TCGA
updated 2.4 years ago by ★ 1.3k • written 2.5 years ago by • 0
1
vote
5
replies
3.3k
views
What statistical test to apply for DE after CibersortX deconvolution
cibersortx differential-expression t-test deconvolution
2.1 years ago by Aspire ▴ 390
13
votes
22
replies
5.7k
views
Help with error in GATK variant calling
GATK
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 360
0
votes
5
replies
2.3k
views
Problem with the output of Deeptools PlotProfile: a strange pattern of repetitive summits
deeptools plotprofile ChIP-seq
updated 2.4 years ago by • 0 • written 3.4 years ago by • 0
1
vote
3
replies
1.4k
views
GRange: Average Metadata Value from 3 Replicates
rtracklayer GenomicRanges GRange
2.4 years ago by RelativeOptics ▴ 40
1
vote
1
reply
1.6k
views
Prefecth-orig and fasterq-dump not working when downloading SRA files (v3.0.5)
Windows SRAtoolkit sra
updated 2.4 years ago by 45k • written 2.4 years ago by • 0
121,991 results • Page 260 of 2440
Recent Votes
A: Trimmomatic Error: Unable to detect quality encoding
A: Trimmomatic Error: Unable to detect quality encoding
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
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Recent Replies
Answer: SNP calling ONT sequenced files by cfos4698 ★ 1.2k
My personal preference is using [clair3][1]. I'm unsure if CLC didn't work because your compute resources are too limited, or if there are …
Comment: HIV NL4-3 transcriptome fasta by Ales ▴ 50
Hi, Wanted to update here that full transcriptome annotations for thousands of hiv genomes (including NL4-3) are now available at https://…
Answer: HIV NL4-3 transcriptome fasta by Ales ▴ 50
You can get full transcriptome annotation for the NL4-3 genomes: https://ccb.jhu.edu/HIV_Atlas/11676/AF324493.2 . Note the accession ID tho…
Answer: Doubt on docking by Mensur Dlakic ★ 30k
I think you are wrongly assuming that we can help you with this without knowing what is the protein of interest. A general answer is that …
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…
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