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3,213 results • Page 4 of 65
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5
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11
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3.4k
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Locating IBD candidates with just VCF files
Relatedness Genotypes IBD Haplotypes VCF
9 months ago by Joel Wallenius ▴ 220
2
votes
11
replies
6.9k
views
8 follow
How to convert and annotate apt-probeset-genotype into PLINK format
PennCNV SNP CNV Affymetrix6 PLINK
updated 6 months ago by • 0 • written 9.7 years ago by ▴ 30
1
vote
11
replies
4.8k
views
Pseudobulk analysis using AggregateExpression()
seurat pseudobulk sum aggregateexpression
updated 11 weeks ago by • 0 • written 13 months ago by • 0
44
votes
11
replies
8.8k
views
8 follow
What are the advantages of using the T2T as a reference vs GRCh38 today?
reference GRCh38 t2t calling variant
updated 4 months ago by 4.8k • written 2.6 years ago by ▴ 170
6
votes
11
replies
11k
views
6 follow
ATAC-seq fragment size distribution - huge spike at 150 bp
ATAC-seq
updated 9 weeks ago by • 0 • written 3.7 years ago by ▴ 10
0
votes
11
replies
1.2k
views
Current size of blast nr database as FASTA file
fasta blast
updated 3 months ago by 16k • written 3 months ago by • 0
0
votes
11
replies
9.8k
views
7 follow
CIBERSORTx error: 'x' must be an array of at least two dimensions
signature CIBERSORTx matrix
updated 9 weeks ago by 90k • written 3.4 years ago by • 0
40
votes
11
replies
7.1k
views
12 follow
What Are Your Most-Used Public Data Repositories?
database
updated 3 months ago by 90k • written 12.3 years ago by 27k
4
votes
11
replies
2.1k
views
Counts after using feature counts is low
hisat2 featureCounts lowcounts
updated 11 months ago by 154k • written 11 months ago by ▴ 70
4
votes
11
replies
2.2k
views
Seeking a tool for enrichment of a small list of ranked genes
enrichment
11 months ago by Aspire ▴ 390
8
votes
11
replies
3.8k
views
is there publicly available tool for assembly of bionano data
OM bionano assembly alignment
12 weeks ago by eebloom ▴ 110
0
votes
11
replies
1.4k
views
Error Correction with Tadpole and BBMerge
BBmerge tadpole error correction
4 months ago by Jon • 0
5
votes
11
replies
4.7k
views
6 follow
Trimming nanopore reads
trim nanopore
updated 7 months ago by 154k • written 21 months ago by ▴ 10
6
votes
11
replies
1.8k
views
Larger genome size than expected-please help
genome nanopore size minimap2
7 months ago by alexandrakortsi • 0
8
votes
10
replies
2.0k
views
Per Sequence GC Content fail
fastqc
7 months ago by Eduardo ▴ 20
14
votes
10
replies
1.6k
views
Does edgeR supports random effects?
RNASeq voom randomeffects edgeR limma
3 months ago by 406339165 ▴ 10
6
votes
10
replies
2.7k
views
6 follow
High Detection of Duplication in RNAseq dataset
Deduplication RNAseq
updated 11 months ago by 22k • written 14 months ago by • 0
11
votes
10
replies
5.5k
views
7 follow
Looking for neanderthal genomes to download
neanderthal neanderthal genome fasta
updated 3 months ago by ▴ 30 • written 9.4 years ago by ▴ 110
53
votes
10
replies
41k
views
9 follow
How is the design in DESeq2 work?
deseq2
updated 9 months ago by 45k • written 8.1 years ago by ★ 2.1k
18
votes
10
replies
3.8k
views
8 follow
scRNAseq Differential expression analysis
scRNA-seq Differential-Expression Seurat
updated 10 weeks ago by 90k • written 2.2 years ago by ▴ 20
1
vote
10
replies
1.4k
views
How to test the similarity of two gene expression profiles
gene-sets
updated 7 months ago by 45k • written 7 months ago by ▴ 20
2
votes
10
replies
1.2k
views
Annotation Issue using miRBASE gff
NGS miRNA
updated 5 months ago by 154k • written 5 months ago by ▴ 30
7
votes
10
replies
2.0k
views
ChromHMM - annotation of chromatin states
state Annoation
updated 9 months ago by 36k • written 10 months ago by • 0
4
votes
10
replies
8.4k
views
Calling star alleles with PGx-POP on my VCF file
vcf alleles pgx-pop star
updated 10 weeks ago by ▴ 40 • written 3.3 years ago by ▴ 50
6
votes
10
replies
3.9k
views
Minimap2 error in Flye de novo assembly
Flye Minimap2
6 months ago by Nilo ▴ 20
9
votes
10
replies
1.5k
views
Making more complex design in limma removes significant genes
limma
updated 25 days ago by ★ 8.6k • written 28 days ago by ▴ 50
77
votes
10
replies
197k
views
8 follow
Fold change - a final explanation
RNA-Seq
updated 6 months ago by 22k • written 7.1 years ago by ▴ 350
0
votes
10
replies
1.4k
views
Errors with RSEM/bowtie2
RNA-seq bowtie2 RSEM Trinity
updated 5 days ago by 90k • written 6 weeks ago by • 0
1
vote
10
replies
4.9k
views
Bedmethyl file format
bedmethyl methylation
updated 8 months ago by • 0 • written 19 months ago by ▴ 20
5
votes
10
replies
1.5k
views
constructing de novo assembly of plant short reads
short reads assembly plants
9 months ago by analyst ▴ 70
3
votes
10
replies
1.8k
views
Nanopore sequencing - plasmid assembly length confusion
assembly long nanopore reads
8 months ago by abedkurdi10 ▴ 190
4
votes
10
replies
1.9k
views
Single-cell dimensionality reduction and clustering
Seurat
updated 11 months ago by 90k • written 11 months ago by ▴ 10
0
votes
10
replies
231
views
Count unique fragments from a given BAM file
dna bam
updated 2 hours ago by 154k • written 6 hours ago by ▴ 520
1
vote
10
replies
2.8k
views
Supergnova stuck in tutorial
Genetic Correlations Python Supergnova Conda
updated 5 months ago by • 0 • written 3.2 years ago by ▴ 10
3
votes
10
replies
2.1k
views
Error in conversion of ensembl to gene names
Ensembl BioMart
updated 11 months ago by 103k • written 11 months ago by ▴ 140
3
votes
10
replies
4.2k
views
TOM matrix generated by WGCNA package in R
WGCNA
updated 10 months ago by 154k • written 3.7 years ago by • 0
4
votes
10
replies
1.8k
views
Batch correction of two RNA-Seq data sets
DESeq2 batch-correction
11 months ago by gogeni5529 ▴ 80
6
votes
10
replies
1.6k
views
6 follow
Snakemake config errors
slurm hpc snakemake
updated 9 months ago by 15k • written 9 months ago by ▴ 30
2
votes
10
replies
2.3k
views
Proper preprocessing for ML after limma, quantile normalization and log2 transformation: Is standardization still necessary?
featureselection microarray preprocessing
updated 6 months ago by ★ 30k • written 7 months ago by ▴ 80
9
votes
10
replies
7.2k
views
11 follow
Forum: insert figure and code in the post of Biostars?
meta biostars
updated 11 months ago by ▴ 10 • written 10.5 years ago by ★ 2.2k
9
votes
10
replies
6.7k
views
7 follow
Buy PC for metagenomics
Assembly alignment genome next-gen
updated 9 months ago by 22k • written 7.4 years ago by ▴ 10
57
votes
10
replies
63k
views
11 follow
ClusterProfiler : What is GeneRatio and BgRatio?
clusterProfiler
updated 5 months ago by ▴ 20 • written 9.0 years ago by ▴ 590
5
votes
10
replies
5.9k
views
6 follow
RNA-SEQ where only a subset of genes is of interest
RNA-Seq deseq
updated 8 weeks ago by • 0 • written 5.2 years ago by ▴ 390
6
votes
10
replies
1.6k
views
building snpeff database for plant
plant
updated 6 months ago by 16k • written 6 months ago by ▴ 70
1
vote
10
replies
1.9k
views
How to create a command that matches 13 characters in each column to be extracted into a new file, and leave behind the unmatched ones
featureCounts
updated 8 months ago by 45k • written 8 months ago by • 0
8
votes
10
replies
2.7k
views
PCA proteomic DEP
PCA DEP
updated 10 days ago by 90k • written 2.2 years ago by ▴ 370
9
votes
10
replies
1.6k
views
STAR vs. Kallisto
STAR kallisto alignment RNA-Seq mapping
updated 6 months ago by ★ 7.8k • written 6 months ago by ▴ 80
5
votes
10
replies
1.5k
views
Need help using ExpansionHunter
ExpansionHunter
4 months ago by brianhill_nc • 0
4
votes
10
replies
4.8k
views
SRA-toolkit installation: "fastq-dump not found"
fastq SRA-toolkit
updated 10 months ago by 154k • written 2.4 years ago by • 0
4
votes
10
replies
1.6k
views
Question about an alignment
ces sequencing alignment
7 months ago by barslmn ★ 2.5k
3,213 results • Page 4 of 65
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Answer: How can I merge GFF files together to produce a file with gene functions from bo
Answer: Running snpEff with hg19 reference genome (config file question)
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
A: DESeq2: vst() and varianceStabilizingTransformation()
Answer: Why do I observe a large number of “Unassigned_NoFeatures” reads in featureCount
Answer: Ribo-seq Trimming Issue: Massive Read Loss in Paired-end Mode
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Recent Replies
Comment: PacBio raw data trimming and cleaning by lieven.sterck 16k
on top of what @genomax says: don't let yourself be fooled by the binning in FastQC graphs, it's a reoccurring thing to be mislead by the b…
Comment: PacBio raw data trimming and cleaning by GenoMax 154k
Don't use/rely on FastQC for long read data. As noted in other comments use a tool meant for long read data.
Comment: PacBio raw data trimming and cleaning by Serena • 0
I think it's CLR data, but not 100% sure. And I got this creepy result of FastQC report and really don't know how to do quality trimming..T…
Comment: 10x Cell Ranger Multi by zizigolu ★ 4.4k
Sorry which file you are kindly referring to (when you mention example barcodes) ? I have been using this file https://cf.10xgenomics.co…
Answer: Count unique fragments from a given BAM file by GenoMax 154k
> a tool to count unique fragments from a given BAM file? This can be a bit tricky. You can imagine a situation where you may have two fr…
Comment: 10x Cell Ranger Multi by zizigolu ★ 4.4k
Thanks a lot But in this section cmo-set Optional. The default CMO reference IDs are built into the Cell Ranger software and do not …
Comment: 10x Cell Ranger Multi by ATpoint 90k
Looking at the examples https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/running-pipelines/cr-3p-multi#hashing -- I…
Comment: Count unique fragments from a given BAM file by lieven.sterck 16k
exactly, first make unique and then count them :) (don't think there is any that does this in one go)
Comment: Count unique fragments from a given BAM file by Ankit ▴ 520
No I got the logic make unique and count
Comment: Count unique fragments from a given BAM file by Ankit ▴ 520
That wont count unique fragments. It will just count coverage
Comment: Count unique fragments from a given BAM file by Ankit ▴ 520
Sure I will look into. Thanks
Comment: Count unique fragments from a given BAM file by lieven.sterck 16k
@ankit : do also take a minute to look at what @yokofakun asked ! (that would be much appreciated ;-) , thanks )
Comment: Count unique fragments from a given BAM file by lieven.sterck 16k
the most basic one is : samtools view -c <your bam file> (will count everything, omitting you exome info ) a bit more 'advanced' : u…
Comment: Count unique fragments from a given BAM file by Pierre Lindenbaum 166k
comment or validate your previous questions, please. * https://www.biostars.org/p/9494014 * https://www.biostars.org/p/9550025 * https…
Comment: Count unique fragments from a given BAM file by Ankit ▴ 520
Thanks, my data is non UMI for the counting part you can use samtools or alike --counting unique fragments how? any flag /syntax?
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