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121,924 results • Page 80 of 2439
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1
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4
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856
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How can I find fasta sequences for gp120 and gp41?
gp41 gp120 subtypes HIV env
13 months ago by mark.pekarsky ▴ 20
5
votes
5
replies
1.1k
views
Pcoa plot
Pcoa
updated 13 months ago by ★ 19k • written 13 months ago by • 0
6
votes
10
replies
1.9k
views
Low mapping rate using SALMON
RNA-SEQ
updated 13 months ago by 153k • written 13 months ago by ▴ 130
1
vote
3
replies
1.5k
views
If TPM is not comparable across cohorts, can it be used as the input for ML models if we have RNASeq data from multiple cohorts?
TPM RNA-seq machine-learning
updated 13 months ago by 5.1k • written 13 months ago by ▴ 10
1
vote
1
reply
1.9k
views
Demultiplex fastq sequences based on sequence header
demultiplexing barcodes fastq Nanopore
updated 13 months ago by 153k • written 13 months ago by • 0
0
votes
0
replies
437
views
News: course on Generalized Linear Mixed Models in R
R Dharma Mixed-Models GLLM
13 months ago by Physalia-courses ★ 2.6k
0
votes
0
replies
796
views
Job: Computational/Bioinformatics Solutions for CRISPR Screening
CRO
updated 13 months ago by 153k • written 13 months ago by ▴ 20
2
votes
6
replies
1.6k
views
How to convert .sdf files into .sdf.gz?
file-conversion
13 months ago by Sanjukta • 0
1
vote
0
replies
552
views
News: Core_nt: new default database for NCBI nucleotide BLAST
core_nt NCBI blastn
13 months ago by EricS_NCBI ▴ 10
0
votes
3
replies
1.7k
views
Cibersort input data
cibersort
updated 13 months ago by ★ 4.4k • written 21 months ago by • 0
1
vote
2
replies
741
views
homo sapiens VCF
Alignment homo-sapiens vcf
updated 13 months ago by 45k • written 13 months ago by • 0
0
votes
0
replies
460
views
News: Check Out Our New Desktop App for scRNA-seq Data Analysis – Beta Testers Wanted!
scRNAseq
13 months ago by OmnibusX ▴ 100
3
votes
2
replies
890
views
Can I Use SureSelect v7 on Exome Data Captured with SureSelect v6?
SureSelect hg38 WES SV
13 months ago by George ▴ 20
3
votes
2
replies
711
views
Finding gtf file for safflower
gtf safflower
13 months ago by analyst ▴ 70
4
votes
8
replies
2.6k
views
Help in Log2 transform CPM count
R edgeR dge Deseq2
updated 13 months ago by 45k • written 13 months ago by ▴ 60
0
votes
1
reply
843
views
Job: Postdoctoral Fellow in Machine Learning for Neuroimaging Genomics at University of Otago – Dunedin, New Zealand
human-genomics machine-learning neuroimaging
13 months ago by narun.pat • 0
1
vote
1
reply
587
views
How to make local BLAST sequentially look through a large number of databases and generate a file for each
BLAST
updated 13 months ago by 153k • written 13 months ago by • 0
0
votes
1
reply
2.3k
views
Problems with overlapping variants in a vcf file
bcftools variant vcf
updated 13 months ago by 45k • written 4.7 years ago by ▴ 10
2
votes
1
reply
764
views
Removing / Excluding / Collapsing Overlapping Indels
bcftools genome vcf genotyping gatk
13 months ago by jon.klonowski ▴ 210
2
votes
5
replies
2.2k
views
GATK SelectVariants consider spanning/overlapping deletions as SNP
SelectVariants SNP gatk INDEL
updated 13 months ago by ▴ 210 • written 4.4 years ago by ▴ 290
0
votes
1
reply
390
views
Contrasting multiple tissues in DiffBind
DiffBind ChIP-seq
updated 13 months ago by 45k • written 13 months ago by • 0
1
vote
1
reply
615
views
Common SNP/variome-aware restriction digest generator for human genome
variome SNP restriction-enzyme
updated 13 months ago by 45k • written 13 months ago by ▴ 490
2
votes
4
replies
3.5k
views
Create Seurat Object from matrix and two text files
Single-Cell RNA-Seq Seurat
updated 13 months ago by ▴ 10 • written 23 months ago by ▴ 10
2
votes
3
replies
844
views
Confusion during BARCODE MATCHING.
primers metagenomics barcode
updated 13 months ago by 153k • written 13 months ago by • 0
1
vote
1
reply
1.0k
views
Creating a signature matrix using CibersortX
CibersortX deconvolution
updated 13 months ago by ★ 19k • written 13 months ago by ▴ 390
2
votes
2
replies
1.6k
views
Plotting LD heat map with plink.ld result
R
13 months ago by selplat21 ▴ 20
1
vote
0
replies
468
views
What exactly is Biopython's alignment.score variable?
Biopython
13 months ago by Tom ▴ 50
1
vote
0
replies
312
views
What happens to M-phase cells in single nucleus RNA-seq?
10X multiome snRNAseq
13 months ago by mpiersonsmela ▴ 20
2
votes
4
replies
1.7k
views
Interpretation of PRS scores calculated from PGS Catalog
PRS PGS-Catalog
updated 13 months ago by ▴ 440 • written 20 months ago by ▴ 30
0
votes
4
replies
1.1k
views
Expression quantification = how is it possible that the amount of sequenced reads assigned to a specific gene/transcript
RNA-seq quantification
updated 13 months ago by 6.5k • written 13 months ago by • 0
0
votes
1
reply
684
views
Polygenic risk score percentile cutoff
GWAS Odds Beta
updated 13 months ago by ▴ 440 • written 19 months ago by • 0
0
votes
1
reply
1.3k
views
Calculating PRS from pre-computed PGS Catalog
GWAS PRS PGS
updated 13 months ago by ▴ 440 • written 23 months ago by ▴ 380
1
vote
1
reply
576
views
QC for UKB GWAS data
UKB GWAS QC
updated 13 months ago by ★ 3.1k • written 13 months ago by • 0
27
votes
9
replies
42k
views
7 follow
How To Extract Set Of Reads From Fastq (Or Eventually Fasta And Qual) Based On List Of Ids?
extraction read 454 fastq fasta
updated 13 months ago by 153k • written 13.4 years ago by 3.2k
0
votes
0
replies
447
views
Can a Binary Signature Matrix Be Used in CIBERSORT for Deconvolution?
regression svm CIBERSORT svr
13 months ago by DareDevil ★ 4.4k
2
votes
3
replies
898
views
Manually creating a valid VCF File
vcf-validator vcf
updated 13 months ago by 6.5k • written 13 months ago by • 0
3
votes
2
replies
944
views
Extraction of miRNA Sequences from Infernal cmscan Output Using Python
infernal assembly rna genome mirna
updated 13 months ago by ▴ 650 • written 13 months ago by ▴ 100
9
votes
12
replies
2.9k
views
7 follow
Forum: What bioinformatics codes would you use for performance benchmarking on a new system?
benchmarking
13 months ago by Dave Carlson ★ 2.2k
2
votes
3
replies
1.9k
views
Beagle imputation error
imputation Beagle
13 months ago by PKW ▴ 110
2
votes
5
replies
1.6k
views
BioPython - qblast() timeout every time, running from python shell
qblast biopython blast ncbi
13 months ago by Ryan • 0
0
votes
0
replies
579
views
News: Population Genomics course (online)
NGS PopulationGenomics Introgression LandscapeGenomics GWAS
13 months ago by Physalia-courses ★ 2.6k
3
votes
6
replies
1.6k
views
how to effectively pipe chromap into samtools view
samtools bash pipe
13 months ago by Matteo Ungaro ▴ 130
1
vote
1
reply
955
views
Batch correction of whole genome bisulfite methylation data
WGBS
updated 13 months ago by ▴ 240 • written 4.2 years ago by ▴ 90
3
votes
11
replies
2.4k
views
6 follow
How to solve DESeq2 Error in checkFullRank(modelMatrix) cause by biological replicates information?
DESEq2 DESEq
updated 13 months ago by 15k • written 13 months ago by • 0
6
votes
5
replies
1.2k
views
Best workflow for identification of isoforms and splice variants
isoforms RNA-seq variants splice
updated 13 months ago by ★ 7.7k • written 13 months ago by ▴ 10
0
votes
0
replies
418
views
does genomics_general.py need both invariant sites and variant sites to calculate pi, FST and DXY
genomics_general
13 months ago by Maxine ▴ 50
0
votes
1
reply
610
views
CLC Genomics workbench and dbSNP VCF import
VCF
updated 13 months ago by 153k • written 13 months ago by • 0
0
votes
0
replies
415
views
Adding and removing sequences in Repeatmasker library (modifying library)
repeatmasker genome repeats
updated 13 months ago by 45k • written 13 months ago by • 0
2
votes
2
replies
848
views
Whole Metagenome Analysis
Metagenomics
13 months ago by karthick ▴ 10
0
votes
1
reply
2.0k
views
Clarification on WGCNA Module-Trait Correlations, Interpretation, and Functional Annotation
WGCNA
updated 13 months ago by 5.1k • written 13 months ago by • 0
121,924 results • Page 80 of 2439
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Comment: Chimera removal dilemma in 16S V3–V4: necessary when using Kraken2/Bracken?
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Recent Replies
Comment: Orthofinder Not Mapping to Any Orthogroups by saamhasan55 ▴ 10
I checked the file and it's definitely proteins. I had previously run BUSCO on protein mode on the same file and got >90% completeness. I r…
Comment: Orthofinder Not Mapping to Any Orthogroups by saamhasan55 ▴ 10
I ran BUSCO on the predicted proteome in protein mode and got >91% completeness. I also removed multiple isoforms from the same gene.
Comment: Help with Model by Stele • 0
Hey, thanks for the reply! I think I didn't make the question very understandable. I do know how to code for this, the wall I have hit is *…
Comment: Orthofinder Not Mapping to Any Orthogroups by Mensur Dlakic ★ 30k
Not enough detail to make a definitive recommendation. Since this should not happen, an educated guess is that you are doing something wron…
Comment: Orthofinder Not Mapping to Any Orthogroups by Michael 56k
A reason may be that your gene prediction is off. Did you run BUSCO on your predicted proteome? If the gene prediction is ok, then you shou…
Comment: Genome Assembly QC from BAM files by GenoMax 153k
> Can you comment on these, If they look good ? More importantly how do these assemblies compare (contiguous/number of chromosomes/size) t…
Comment: TOPMed Imputation - More than 10000 allele switches by Qianshu • 0
Hi, I have the same error with you, have you sorted it out yet? If you have, could you please share some? Thank you!
Comment: Genome Assembly QC from BAM files by colindaven 7.9k
yes they look excellent
Comment: Genome Assembly QC from BAM files by SomeOne ▴ 240
hello @colindaven I ran the INSPECTOR tool you mentioned on the genome assemblies. Below are stats for one of my sample (othere were simi…
Comment: Chimera removal dilemma in 16S V3–V4: necessary when using Kraken2/Bracken? by Christopher ▴ 10
You are right. I initially decided to keep Cutadapt because I feel more confident using it for primer removal, and it is the tool most comm…
Answer: Help with Model by i.sudbery 22k
I'm not quite sure what you are asking. Stochastic reaction networks like this can be coded using the Gillespie algorithm. Genes being …
Comment: miRNA low mapping ratings by Ant ▴ 50
No, these are from the total reads, but when considering only the reads with adapter, I checked MultiQC again and it’s around 10–20% when a…
Comment: miRNA low mapping ratings by GenoMax 153k
> the total number of reads is very low (around 1–10% of the total reads) Are these the reads that actually have the QIAseq 3'-miRNA adapt…
Comment: Chimera removal dilemma in 16S V3–V4: necessary when using Kraken2/Bracken? by GenoMax 153k
> cutadapt > bbduk > bowtie2 > qiime2 > dada2 > kraken2 > krona Curious as to why you have `cutadapt` and `bbduk`. `bbduk` should be able…
Comment: miRNA low mapping ratings by i.sudbery 22k
As GenoMax said, the most likely thing to me here is that there is nothing cloned into the library. I can't think of any bioinformatic reas…
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