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1.1k
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Explaining my heatmap for PC1 and my PC2 with gene list
pca heatmap
updated 13 months ago by 89k • written 14 months ago by • 0
1
vote
1
reply
1.1k
views
How to deal with warnings from PLINK while performing QC using HAPMAP data ?
QC Hapmap PLINK GWAS
updated 13 months ago by 89k • written 13 months ago by ▴ 10
0
votes
1
reply
1.0k
views
GWAS on traits non-normally distributed
normality GWAS phenotypes
updated 13 months ago by 89k • written 13 months ago by • 0
0
votes
14
replies
3.1k
views
DEseq2 on expected counts
DEseq2 Normalize raw-counts
updated 13 months ago by 89k • written 13 months ago by ▴ 10
0
votes
2
replies
846
views
VCF files
GATK VCF homo-sapiens
updated 13 months ago by 89k • written 13 months ago by • 0
1
vote
1
reply
718
views
Values of relatedness matrix exceed 0 and 1
CGTA matrix snpgdsGRM relatedness
updated 13 months ago by 89k • written 13 months ago by • 0
3
votes
1
reply
806
views
Downloading metadata of all insect SRA sequences from NCBI SRA
database NCBI SRA
updated 13 months ago by 8.9k • written 13 months ago by ▴ 50
1
vote
3
replies
814
views
Pfam only identifies collagen
RNA-seq lncRNA
updated 13 months ago by 45k • written 13 months ago by • 0
0
votes
1
reply
556
views
How to split the aligned output from SortMeRNA into forward and reverse sequences
metatranscriptomic sortmerna
updated 13 months ago by 166k • written 13 months ago by ▴ 20
4
votes
5
replies
1.7k
views
6 follow
Remove part of a header in a fasta file
fasta
updated 13 months ago by ★ 3.1k • written 2.9 years ago by • 0
0
votes
3
replies
2.0k
views
rna-seq heatmap z-score calculation - TPM?
heatmap rnaseq
updated 13 months ago by 89k • written 13 months ago by • 0
0
votes
1
reply
622
views
Sampling distribution of cosine similarity
RNA-seq
updated 13 months ago by ▴ 80 • written 13 months ago by ▴ 10
0
votes
1
reply
496
views
usually retained introns
intron alternative retention splicing
updated 13 months ago by ★ 2.2k • written 13 months ago by ▴ 10
5
votes
2
replies
914
views
How to Handle Unbalanced RNA-seq Data (710 vs. 15 Samples) Using DESeq2?
R DESeq2 Unbalanced RNA-seq groups
updated 13 months ago by ★ 1.9k • written 13 months ago by ▴ 140
5
votes
3
replies
1.1k
views
Benchmark hg19 vcf by hs37d5 vcf
hs37d5 benchmark hg19 GIAB
updated 13 months ago by 166k • written 13 months ago by • 0
0
votes
1
reply
667
views
How do you compare HLA allele frequencies between two populations?
allele-frequency HLA
updated 13 months ago by ★ 3.1k • written 13 months ago by • 0
0
votes
4
replies
947
views
Heatmap for DEGs
seq heatmap RNA
13 months ago by 4732b159 • 0
1
vote
0
replies
474
views
News: RNAseq and Single Cell Analysis Online Courses @ Edinburgh Genomics
RNA-seq single-cell workshop
updated 13 months ago by 45k • written 13 months ago by ▴ 10
0
votes
11
replies
2.2k
views
Convert Gene ID To Gene Name
geneid
13 months ago by min • 0
3
votes
5
replies
1.5k
views
Converting GFA to rGFA
gfa
13 months ago by Ric ▴ 440
2
votes
5
replies
1.2k
views
How to View Peaks from ChIP-seq Data generated using old reference genome (hg18)
R Peak ChIP-seq
updated 13 months ago by 89k • written 13 months ago by ★ 4.4k
0
votes
0
replies
786
views
Blog: Metagenomics: Host DNA Removal or Not?
sequencing. shotgun metagenomics. metagenomic
13 months ago by Novogene ▴ 510
6
votes
8
replies
1.9k
views
How to perform BLASTn on a large 348kb phage genome?
BLASTn
updated 13 months ago by 153k • written 13 months ago by • 0
0
votes
2
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1.5k
views
Apply Plink2 Score - Error Invalid chromosome code
plink plink2 pgsc_calc plink2score
updated 13 months ago by ▴ 10 • written 2.1 years ago by • 0
0
votes
4
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1.6k
views
PLINK error doing a GWAS
phenotype PLINK covariates association GWAS
updated 13 months ago by 11k • written 13 months ago by • 0
1
vote
6
replies
1.5k
views
Analyzing PCA Clustering from PLINK Output
plink
13 months ago by Smriti ▴ 40
7
votes
17
replies
5.0k
views
Current best practive to liftOver many SNVs from hg19 to GRCh38
liftOver
12 months ago by User 7754 ▴ 290
4
votes
6
replies
1.5k
views
gene naming
gene-names ensembl blast
updated 12 months ago by 153k • written 13 months ago by ▴ 10
1
vote
3
replies
1.2k
views
Affymetrix microarray
gene-expression probes microarray
updated 13 months ago by 45k • written 13 months ago by ▴ 10
0
votes
2
replies
912
views
Why does 1 variant produce 3 genes as a result?
GATK SnpEff
updated 13 months ago by 89k • written 13 months ago by ▴ 60
0
votes
4
replies
1.4k
views
6 follow
Batch correction in RNAseq
RNA-seq batch-correction
updated 13 months ago by 89k • written 13 months ago by • 0
2
votes
1
reply
910
views
WGCNA - dendogram: How to interpret alterations of clusters
clustering transcriptomics WGCNA rna
updated 13 months ago by 45k • written 13 months ago by • 0
0
votes
1
reply
1.1k
views
Batch Effect Correction in RNA-seq Data Using SVA and DESeq2
SVA Batch DESeq2 RNA-seq
updated 13 months ago by 89k • written 13 months ago by ▴ 20
0
votes
0
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452
views
News: Phylogenomics course
Multispecies-Coalescent-Model Bayesian-Inference Phylogenomics Divergence-Time Maximum-Likelihood
updated 13 months ago by 45k • written 13 months ago by ★ 2.6k
1
vote
1
reply
565
views
Ethnicity information in GTEx dataset
metadata gtex
updated 13 months ago by 153k • written 13 months ago by ▴ 410
1
vote
1
reply
519
views
How can I flag possible errors in the handbook collection?
Feedback
updated 13 months ago by 166k • written 13 months ago by ▴ 10
0
votes
2
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816
views
RNA-seq and Chip Seq alignment
ChIP-seq RNA-seq alignment
updated 13 months ago by 45k • written 13 months ago by • 0
12
votes
6
replies
8.7k
views
Download Hg18 Snp Database
snp
updated 13 months ago by ★ 4.4k • written 14.4 years ago by ▴ 140
4
votes
4
replies
1.9k
views
Microbial PacBio metagenomes and MAG pipeline (assembly/binning) METABAT
binning mag pacbio metabat
updated 13 months ago by ▴ 40 • written 13 months ago by ▴ 20
0
votes
0
replies
856
views
Job: Job opening for a Computational Biologist position at Weill Cornell Medical College, New York , USA
Computational-Genomics Cornell Transcriptomics GI-Oncology
updated 13 months ago by 45k • written 13 months ago by • 0
1
vote
10
replies
1.9k
views
ncRNA database for mus
contamination ncRNA sequencing
updated 13 months ago by ▴ 450 • written 13 months ago by ▴ 40
0
votes
1
reply
2.0k
views
Seurat V5 Subscript Out of Bounds Error
Seurat scRNA
updated 13 months ago by ★ 3.1k • written 13 months ago by • 0
1
vote
0
replies
730
views
News: Course - Machine Learning for Multi-Omics Integration
Machine-Learning Big-Data Multi-Omics Data-Integration Deep-Learning
updated 13 months ago by 45k • written 13 months ago by ★ 2.6k
1
vote
4
replies
1.1k
views
Overlapping reads between two BED windows
samtools bam bedtools coverage
13 months ago by pablo ▴ 350
0
votes
0
replies
391
views
Are there reliable assays other than genome sequencing, to measure tumor heterogeneity?
NGS tumor-heterogeneity WGS
updated 13 months ago by 45k • written 13 months ago by ▴ 20
1
vote
1
reply
699
views
Gene Regulatory Network Inference Data Needed
GRN scATAC-SEQ scRNA-SEQ Single-Cell Gene-Regulatory-Networks
updated 13 months ago by 45k • written 13 months ago by ▴ 110
1
vote
1
reply
730
views
Remove microbes(cobionts) contamination: before or after insect de novo genome assembly?
contamination genome assembly
updated 13 months ago by 8.9k • written 13 months ago by • 0
3
votes
9
replies
5.5k
views
6 follow
Error Muscle alignment (msa package, through Rscript)
msa r muscle
updated 13 months ago by ▴ 10 • written 5.4 years ago by ▴ 10
1
vote
1
reply
511
views
Metatranscriptome pipeline: taxonomy and functional recover
metatranscriptome pipeline phyloflash
updated 13 months ago by • 0 • written 13 months ago by ▴ 20
2
votes
5
replies
1.2k
views
SNPs are not detected.
bcftools SNP WGS
updated 13 months ago by 166k • written 13 months ago by ▴ 10
121,923 results • Page 76 of 2439
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Comment: Chimera removal dilemma in 16S V3–V4: necessary when using Kraken2/Bracken?
C: Counting Number Of Bases In A Fastq File
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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…
Comment: miRNA low mapping ratings by Ant ▴ 50
Sorry, I gave you answers based on different samples. The thing is, the total number of reads is very low (around 1–10% of the total reads)…
Comment: miRNA low mapping ratings by Ant ▴ 50
Yes, it was in 75bp. I don1t know if it was the first time he used the kit, but I remember he needs to adjust the protocol.
Comment: SNP calling with bacterial assembled genome by GenoMax 153k
> Is it possible to do this at the assembly level? By aligning to a reference you can find the differences between your assembly and the …
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