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121,984 results • Page 643 of 2440
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gene expression for a specific gene across for multiple cancer types in TCGA datasets
gene_expression TCGA RTCAG
4.4 years ago by pt.taklifi ▴ 70
0
votes
4
replies
4.1k
views
Flye assembly of a bacterial genome stuck
assembly Flye
updated 4.4 years ago by 3.9k • written 4.4 years ago by ▴ 170
2
votes
4
replies
7.2k
views
Difficulty filtering VCF file with vcftools
SNP
updated 4.4 years ago by ▴ 480 • written 9.0 years ago by ▴ 110
1
vote
2
replies
2.0k
views
KING relatedness inference working way too long...
large-cohort
4.4 years ago by German.M.Demidov ★ 3.0k
0
votes
4
replies
1.9k
views
Issue with memory and the gcsa index in toil-vg
toil-vg vg vgteam
4.3 years ago by jcmouren • 0
0
votes
2
replies
974
views
RNA-seq different reads numbers of two samples is trouble?
RNA-Seq R seq python linux
updated 4.4 years ago by ★ 1.4k • written 4.4 years ago by ▴ 10
0
votes
0
replies
793
views
How to merge the mutations from multiple samples of one patient
MutSig2CV_NC MutSig2CV cancer mutation merge
4.4 years ago by Rongxin ▴ 40
0
votes
9
replies
3.9k
views
Using wildcards in function in rules
snakemake rules wildcards
updated 4.4 years ago by ▴ 160 • written 4.4 years ago by ▴ 10
4
votes
7
replies
5.8k
views
6 follow
Tool: MAGERI: a software tool for calling rare variants and detecting circulating tumor DNA from UMI-tagged high-throughput sequencing data
rare-variant resequencing umi ctDNA
updated 20 months ago by • 0 • written 8.4 years ago by 3.5k
0
votes
0
replies
869
views
Avoid genome circularization with Canu assembler
circularization ONT Canu repetitive-regions assembler
updated 18 months ago by 45k • written 4.4 years ago by • 0
0
votes
1
reply
999
views
read ids along with transcript ids
stringtie flair read correction nanopore
updated 4.4 years ago by 103k • written 4.4 years ago by • 0
0
votes
0
replies
689
views
Emperical frequencies in BEAST2
model BEAST
4.4 years ago by Vasiliy Krestov ▴ 30
0
votes
0
replies
844
views
Cut&Run fragment length
CutAndRun
updated 2.6 years ago by 45k • written 4.4 years ago by ▴ 30
3
votes
6
replies
2.6k
views
Is Ensembl VEP down right now?
Ensembl VEP
updated 4.4 years ago by ▴ 290 • written 4.4 years ago by ▴ 480
3
votes
5
replies
1.7k
views
How do I write the regex expression for the line?
regex
updated 4.4 years ago by 14k • written 4.4 years ago by • 0
0
votes
1
reply
1.5k
views
Tutorial: Add Customized Filters in GDC
gdc
updated 4.4 years ago by 21k • written 4.4 years ago by ★ 1.3k
2
votes
3
replies
1.8k
views
How to Align multiple short reads (NGS data) to a short (~200bp) reference?
genomics NGS CRISPR genotyping
updated 4.3 years ago by 45k • written 4.4 years ago by ▴ 10
0
votes
1
reply
6.0k
views
PCoA vs NMDS
NMDS PCoA
4.4 years ago by valentinavan ▴ 50
0
votes
5
replies
1.9k
views
Command Line BLAST Question
phylogenetic line BLAST command
updated 4.3 years ago by 11k • written 4.4 years ago by • 0
3
votes
3
replies
1.8k
views
quick way of contamination identification from fastq file
alignment
updated 4.4 years ago by ★ 1.4k • written 4.4 years ago by ▴ 280
3
votes
5
replies
1.9k
views
Ballgown R Package
R DEGs Ballgown
updated 4.4 years ago by 21k • written 4.4 years ago by • 0
0
votes
0
replies
1.2k
views
Quality score and trimming length in DADA2
QIIME2 DADA2
4.4 years ago by yohannessys • 0
0
votes
0
replies
757
views
Flexibility of protein (ProtParam module from biopython)
biopython Flexibility
4.4 years ago by ja4123 ▴ 30
2
votes
5
replies
4.3k
views
How to use DEGs file for GSEA?
gsea RNA-Seq scRNA-seq Seurat
updated 4.4 years ago by • 0 • written 4.8 years ago by ▴ 90
2
votes
2
replies
1.5k
views
How to combine datasets from different sequencing platforms?
RNASeq Expression Differential Normalization
updated 4.4 years ago by 23k • written 4.4 years ago by ▴ 140
0
votes
0
replies
776
views
News: Online Training -Metabarcoding of microbial communities
Metabarcoding
4.4 years ago by Physalia-courses ★ 2.6k
1
vote
6
replies
1.9k
views
Micro analysis pipeline
RNA-Seq
updated 4.3 years ago by ▴ 90 • written 4.4 years ago by • 0
5
votes
6
replies
2.1k
views
Problem with limma in microarray analysis
limma microarray R
4.4 years ago by reza ▴ 300
0
votes
2
replies
922
views
automatic detection of false-positive large indels checking their GQ scores
preprocessing VCF multisample
4.4 years ago by bio.pelayo • 0
2
votes
6
replies
2.3k
views
Hello everyone whenever i run this command this error terminates the command. can someone please guide me
analysis artic sequencing Minion nanopore
4.3 years ago by mibtisamnasar ▴ 10
5
votes
2
replies
1.9k
views
Assembly oxford nanopore data
assembly oxford nanopore
4.4 years ago by A_heath ▴ 170
2
votes
4
replies
1.5k
views
Snakemake error
GATK Snakemake
4.3 years ago by kamanovae ▴ 100
0
votes
2
replies
2.8k
views
Observation about CIBERSORTx variations in results due to missing genes
CIBERSORTx deconvolution RNA-seq type Cell
3.8 years ago by argonvibio • 0
0
votes
1
reply
1.1k
views
Finding all variant by bcftools call
bcftools variant-calling
updated 2.6 years ago by 45k • written 4.4 years ago by • 0
9
votes
14
replies
3.6k
views
6 follow
Forum: What are the pain points in genomic variant interpretation/annotation processes?
analysis variant
updated 4.2 years ago by ★ 1.3k • written 4.4 years ago by ▴ 90
1
vote
3
replies
1.5k
views
how to properly run TrioCNV for trios CNV detection
github CNV TrioCNV
updated 4.4 years ago by ★ 3.0k • written 4.4 years ago by ▴ 10
0
votes
2
replies
2.8k
views
Correcting for multiple testing: 12 multiple regressions, with several covariates.
bonferroni regression multiple-testing
updated 4.4 years ago by ▴ 940 • written 4.4 years ago by • 0
4
votes
6
replies
4.3k
views
how to keep reads in a fasta file based on a seq id list in R?
R filter fasta
updated 4.4 years ago by 21k • written 4.4 years ago by ▴ 80
3
votes
5
replies
3.2k
views
Install BAliBASE 3 in windows
BAliBASE expat
updated 4.4 years ago by • 0 • written 9.3 years ago by • 0
0
votes
1
reply
871
views
haplotype phasing with SHAPIT
phasing SHAPEIT
updated 4.4 years ago by 2.9k • written 4.4 years ago by • 0
0
votes
0
replies
2.1k
views
Cell Ranger low "Fraction Reads in Cells"
Ranger single cell Cell scRNA
4.4 years ago by Giup • 0
0
votes
6
replies
1.6k
views
Delete Biosamples and Organism in Tripal
database tripal
updated 3.1 years ago by • 0 • written 4.4 years ago by ▴ 120
0
votes
6
replies
1.9k
views
how to indentify unannotated exon-exon junction from a bam/sam file
RNA-seq junction exon-exon
updated 4.4 years ago by 22k • written 4.4 years ago by ▴ 30
2
votes
2
replies
3.5k
views
how to edit a .rds file in r?
dataframe r .rds pdata
updated 4.4 years ago by ★ 1.7k • written 4.4 years ago by ▴ 20
0
votes
4
replies
1.3k
views
Python error solve
python
updated 4.4 years ago by 103k • written 4.4 years ago by ▴ 20
1
vote
2
replies
1.2k
views
Converting NCBI refseq ids to ENTREZIDs
Genesymbol refseqids RNAseq ENTREZID
updated 4.4 years ago by ★ 1.7k • written 4.4 years ago by ▴ 10
0
votes
0
replies
700
views
How to use transcript coverage for ORF calls on contig?
gene-calling virus metatranscriptomics metagenomics
4.4 years ago by O.rka ▴ 750
2
votes
1
reply
1.1k
views
BEAST model defaults
model BEAST
updated 4.4 years ago by ★ 30k • written 4.4 years ago by ▴ 30
0
votes
3
replies
1.9k
views
Analyze Linkage disequilibrium between SNPs in a Gene Region using Haploview 4.2
haplotype snp genetics disequilibrium linkage genome
updated 4.3 years ago by ▴ 10 • written 4.7 years ago by ▴ 50
6
votes
4
replies
1.7k
views
Bedops split bed coordinates with zero based half opened format
DNA bedops STREME
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 190
121,984 results • Page 643 of 2440
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Answer: Corresponding BAM files
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Is this an appropriate command for estimating contaminatin in a germline WGS sample using GATK?
Answer: Dorado in PowerShell on Windows
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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…
Answer: 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…
Comment: Hisat2 splice sites extract blank files by Ales ▴ 50
Interestingly, HIV/SIV specifically does have quite an elaborate splicing system which regulates translation. However, only one of the spli…
Answer: Analyzing CRISPR and RNAi genome wide screens by Meisam ▴ 250
I'm late to the party but in case someone has the same question: one practical approach is using **rank-based** methods to meta-analyse you…
Answer: meta data analysis for clustering by Meisam ▴ 250
I'm late to the party but one practical approach is using **rank-based** methods to meta-analyse your screens, which basically bypass the n…
Comment: convert genome file to transcriptome file by Ales ▴ 50
Should be noted that the gtf/gff and genomic.fna files for HIV only contain CDS annotations of the 9 ORFs and not the full transcripts. Onl…
Comment: GTF file for HIV strain pNL4-3 by Ales ▴ 50
just wanted to follow up that to address this specific issue we just released HIV transcriptome annotations of alternative splicing featuri…
Answer: GTF file for HIV strain pNL4-3 by Ales ▴ 50
For anyone stumbling on this. We have recently completed reference-grade annotation for several thousand HIV-1 genomes including the HXB2 (…
Comment: Dorado in PowerShell on Windows by sbissi102 ▴ 10
Yes, I found all the barcodes, but could working on WSL affect the basecalling results?
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions by DdogBoss ▴ 20
Since I was running in stub-run mode, the solution was to make unique names for the FASTQC process like this: touch ${sample}_${rea…
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