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147 results • Page 3 of 3
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163
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Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
5 days ago by ekirsch • 0
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170
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How to root an unrooted tree with a known root tree?
phylogenetics rooting R
5 days ago by P. • 0
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0
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155
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How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score tspex
updated 5 days ago by 43k • written 5 days ago by ▴ 10
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172
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Pruning with plink finds a majority of SNPs in very high LD
LD SNP plink pruning
5 days ago by enferdeflame • 0
0
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0
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207
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Variant Generation Using Longshot
long-reads variant-calling ONT minion longshot
updated 5 days ago by 43k • written 5 days ago by ▴ 10
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0
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2.0k
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NOISeq Batch Correction to RNA-seq data
Batch-effect RNA-Seq ARSyNseq limma NOISeq
updated 5 days ago by 43k • written 6.9 years ago by • 0
0
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0
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1.9k
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Correcting batch effect from known variables in RnBeads using Combat
Combat 450k methylation RnBeads batch-effect
updated 5 days ago by 43k • written 7.1 years ago by ▴ 40
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0
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1.9k
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batch effect in radseq
radseq batch-effect SNP
updated 5 days ago by 43k • written 7.5 years ago by ▴ 50
0
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0
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729
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
RNA-Seq scRNA-Seq batch-effect
updated 5 days ago by 43k • written 3.4 years ago by ▴ 180
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0
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1.2k
views
Batch estimate using kBET
batch-effect kbet
updated 5 days ago by 43k • written 4.0 years ago by • 0
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0
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1.8k
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Differential expression using Scran batch corrected data
single-cell Batch-effect RNA-Seq Scran
updated 5 days ago by 43k • written 5.4 years ago by ▴ 10
0
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0
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208
views
create genewise sync file in popoolation
popoolation
updated 5 days ago by 141k • written 5 days ago by • 0
0
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0
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188
views
miRDeep2: How to get the read counts
mirdeep2
4 days ago by Atul K. • 0
0
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0
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171
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SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs ngsTools ANGSD genomics
4 days ago by DanielEB_fisk ▴ 20
0
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0
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190
views
Conversion to tree format
PLINK bed Figtree SplitsTree
updated 4 days ago by 43k • written 4 days ago by • 0
0
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0
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198
views
Lncipedia GTF file error
Proteomics
updated 4 days ago by 43k • written 4 days ago by ▴ 10
0
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0
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199
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Copy number variation plot
Copy-number-variation genomics
updated 4 days ago by 43k • written 4 days ago by • 0
0
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0
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176
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Chemical structure validation
structure cap validation metabolite
4 days ago by Rodolfo Adrián • 0
0
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0
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183
views
absolute path for symbolic links in Snakefile
Snakemake
updated 4 days ago by 43k • written 4 days ago by ▴ 60
0
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0
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183
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scRNA Cluster frequency
CV PCA scRNA Cluster-Frequency
4 days ago by Nitin • 0
0
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0
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182
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agilent microarray gpl data does not have gene symbol column
microarray agilent gpl
updated 4 days ago by 43k • written 4 days ago by • 0
1
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528
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The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers TRINITY
3 days ago by mathavanbioinfo ▴ 90
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0
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204
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Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools gcs
3 days ago by abhishekghadge • 0
0
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0
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126
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation CGenFF Gromacs VMD
3 days ago by Mamatha Y S • 0
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0
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135
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Bacterial genome alignment with mauve
Bacteria mauve genome
3 days ago by rthapa ▴ 90
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0
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133
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How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 2 days ago by 43k • written 3 days ago by • 0
0
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0
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105
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CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 1 day ago by 8.7k • written 1 day ago by • 0
0
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0
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71
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Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER MARINA ARACNe
1 day ago by Biostars2200 • 0
0
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0
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67
views
Correct way of reducing predictive model complexity
lasso glmnet predictvemodeling regression
1 day ago by sativus ▴ 20
0
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0
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80
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Trimming best practices for SNP calling
trimming SNP trimmomatic
1 day ago by Enrique • 0
0
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0
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64
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Imputation advice
imputation
1 day ago by kl ▴ 10
0
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0
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71
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Annotating single cell data automatically
cell annotation single
1 day ago by Gerard • 0
0
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0
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75
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How to get somatic variation based on RNA-seq data?
RNA-seq variation somatic
1 day ago by feather-W • 0
0
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0
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76
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Help with finding conferences in immuno-informatics/virology
virology conferences immunology
1 day ago by manaswwm ▴ 490
0
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0
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197
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traying to make a maf from an already annotated vcf
vcf vcf2maf maf maftools VEP
1 day ago by Javier • 0
0
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0
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72
views
Analysis of the gene family of a genome.
Genome gene-family
updated 1 day ago by 43k • written 1 day ago by ▴ 80
0
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0
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130
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS Meta-analysis
updated 1 day ago by 43k • written 1 day ago by ▴ 10
0
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0
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271
views
Choice of relatedness cutoff for GWAS of a large cohort (>100K samples)
relatedness IBD GWAS
updated 1 day ago by 43k • written 14 months ago by ▴ 10
0
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0
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86
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment Genomics Ka-Ks
updated 1 day ago by 43k • written 1 day ago by ▴ 200
0
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0
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66
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
13 hours ago by alifafiq1 • 0
0
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0
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56
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Merging replicates from Encode project
CHIP-seq encode
13 hours ago by Nurken • 0
0
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0
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49
views
Software to calculate RSCU, ENC other than codonw
rscu codonw
updated 9 hours ago by 43k • written 12 hours ago by • 0
0
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0
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79
views
File with NCBI summary or Uniprot description
annotation visualisation NCBI Uniprot RNA
updated 9 hours ago by 43k • written 1 day ago by • 0
0
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0
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43
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The concept of co-occurrence network structure
co-occurence microbiome network
9 hours ago by ohtang7 ▴ 40
0
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0
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57
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How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy Copy-number-analysis R
updated 9 hours ago by 43k • written 20 hours ago by • 0
0
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0
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25
views
How to solve this RoseTTAFold colaboratory error?
modeling Google Colaboratory RoseTTAFold protein
3 hours ago by benguyarenbeyaz98 • 0
0
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0
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15
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Wilcox test using data slot (log normalized count values) of scRNA-seq between two groups
scRNAseq
1 hour ago by mropri ▴ 150
147 results • Page 3 of 3
Recent Votes
Answer: HaplotypeCaller - only SNPs
Comment: Bwa sampe - BGI
Comment: Redirection of Duplicate PMIDs
Answer: Redirection of Duplicate PMIDs
A: Should I Remove All Positions Containing A Gap In A Multiple Alignment Prior To
Should I Remove All Positions Containing A Gap In A Multiple Alignment Prior To Creating A Phylogenetic Tree?
Answer: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
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Recent Replies
Answer: HaplotypeCaller - only SNPs by Pierre Lindenbaum 161k
Filter the vcf dowstream after haplotypecaller using bcftools or gatk variantfiltration
Answer: Gene set enrichment analysis differences between 2020 and 2024 by geneontologyhelp ▴ 360
We have releases about monthly in order to keep our data accurate and reflect current understanding. In 4 years, there have been about 40 r…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by GenoMax 141k
Let us know when you find out. Would be a useful thing to know what the data looks like.
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by atowns21 • 0
Yes, that is a very good idea. Thanks for the help!
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by GenoMax 141k
Only thing would be to try them out. See if you can detect them in the data you have. You could also simply look for unique representativ…
Comment: How to calculate identity percentage between proteins contained in a FASTA file? by GenoMax 141k
`clustal omega` can calculate distance matrix between two proteins (makes sense if your proteins are of similar size). You could try that: …
Comment: Should I use unpaired reads from trimmomatic by swbarnes2 14k
If the unpaired are _2, files, the _1 must exist somewhere. But the simple answer is probably going to be to just use all the _2 only. Yo…
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File? by GenoMax 141k
> The needless granularity (fake precision) was obvious from the start You are assuming that all data generated is always of great quality…
Answer: Blasting two protein sequences vs two nucleotide sequences by Istvan Albert 100k
There are various versions of blast, that search in translated spaces, see blastx and tblastn https://blast.ncbi.nlm.nih.gov/Blast.cgi …
Answer: Should I use unpaired reads from trimmomatic by Istvan Albert 100k
If you have lots of data, both paired and unpaired, then the best strategy is probably to treat them separately and merge the counts at the…
Comment: Difference between samtools "-f 9" and "-f 11" by Istvan Albert 100k
It is very easy to make nonsensical flags (unfortunately a flaw of the SAM spec itself) ... not to mention the awkward constructs: a primar…
Comment: Heatmap and rna-seq by Istvan Albert 100k
This forum is dedicated to asking their question on bioinformatics. As long as the topic is bioinformatics, all questions are welcome, and …
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File? by Istvan Albert 100k
I interpret this as an admission by SRA that phred scores are practically useless. The needless granularity (fake precision) was obvious f…
Comment: TCGA2STAT Error: Firehose connection by Ram 43k
If their github repo is alive, raise an issue there.
Comment: TCGA2STAT Error: Firehose connection by Ngrin • 0
Yeah makes sense. I was following their github. Thanks for pointing this out.
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