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Job: Research assistant/postdoc in computational biology/bioinformatics (UMass Medical, Worcester, Massachusetts, USA)
computational genetics genomics
updated 4.4 years ago by 45k • written 4.6 years ago by ▴ 10
0
votes
0
replies
998
views
Error in generating index file using vg index
vg pggb
4.5 years ago by evafinegan • 0
1
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2
replies
1.8k
views
Export error in cytoscape
cytoscape network
4.5 years ago by Madhawa • 0
0
votes
1
reply
897
views
Quantification of non-covalent interactions at protein-protein interfaces
interactions energies PPI Interface Non-covalent
updated 4.5 years ago by ★ 30k • written 4.5 years ago by • 0
0
votes
0
replies
792
views
How can I use statistics to compare microbial phenotypes
statistics microbial-genomics phenotype
4.5 years ago by sagrant ▴ 10
0
votes
0
replies
1.5k
views
getDifferentialPeaksReplicates.pl
NGS ChIP ChipSeq
4.5 years ago by jjp55 ▴ 20
5
votes
3
replies
1.7k
views
RefSeq Annotation Report - Gene and Feature Statistics
gff ncbi gff3 annotation refseq
4.5 years ago by mglasena ▴ 40
4
votes
4
replies
1.3k
views
Reads alignment on human and pathogen combined genome
linux STAR alignment
updated 4.5 years ago by 45k • written 4.5 years ago by • 0
1
vote
2
replies
2.4k
views
GWAS QC step - Heterozygosity
heterozygosity GWAS PLINK ImagingGenetics
4.5 years ago by jun0914 ▴ 10
1
vote
2
replies
3.0k
views
how to get total number of reads in a IGV view
igv
updated 4.5 years ago by 154k • written 4.5 years ago by ▴ 80
0
votes
2
replies
1.9k
views
No peaks in CUT&RUN
bowtie2 ngs chip-seq SEACR
4.5 years ago by Johanna • 0
0
votes
2
replies
1.0k
views
How use gprofiler2 ourput visulize in Cytosape
GO pathway Cytoscape gprofiler2
4.5 years ago by BISEP ▴ 10
0
votes
3
replies
1.6k
views
Gene duplication analysis in plants
gene duplication genome
4.5 years ago by umeshtanwar2 ▴ 30
11
votes
5
replies
4.2k
views
Deseq same padj values for a lot of genes but with different p-values
Deseq RNA-seq
updated 3.8 years ago by ★ 19k • written 4.5 years ago by ▴ 20
3
votes
11
replies
2.9k
views
How can I pull out specific protein fastas from one file using information from the protein header?
protein grep accession fasta
updated 4.5 years ago by 21k • written 4.5 years ago by ▴ 50
0
votes
0
replies
1.6k
views
terminate called after throwing an instance of 'std::logic_error' in TreeMix
phylogeny treemix phylogenetics
4.5 years ago by hemr3 ▴ 10
2
votes
4
replies
1.9k
views
Error in read.celfile.header(x)
package oligo rstudio microarray r
updated 4.5 years ago by 21k • written 4.5 years ago by ▴ 20
2
votes
4
replies
3.5k
views
Installing Bedtools with Cygwin fails.
cygwin bedtools
updated 4.5 years ago by ★ 19k • written 7.1 years ago by ▴ 110
1
vote
7
replies
2.3k
views
Cannot able to find a particular column in R
dataframe r bioconductor microarray
updated 4.5 years ago by 21k • written 4.5 years ago by ▴ 20
1
vote
2
replies
1.4k
views
bcftools isec outputs all variants instead of just the common variants
output intersection bcftools isec
4.5 years ago by fafad046 • 0
0
votes
0
replies
878
views
Problem with GATK VariantFiltration
gatk snakemake
4.5 years ago by kamanovae ▴ 100
0
votes
0
replies
734
views
Uniquely mapped reads on Bowtie for colorspace RNA-seq
uniquely bowtie RNA-seq samtools
updated 4.5 years ago by 35k • written 4.5 years ago by • 0
0
votes
1
reply
2.6k
views
GSEA analysis error: unable to find an inherited method for function ‘species’ for signature ‘"character"’
gsea R Bioconductor
updated 4.5 years ago by 12k • written 4.5 years ago by • 0
2
votes
4
replies
1.7k
views
RNA Seq
Isoform Quantification
updated 4.5 years ago by ★ 19k • written 4.5 years ago by ▴ 40
47
votes
21
replies
31k
views
14 follow
LD-decay in a r2 vs distance(cm) plot
R snp
updated 4.5 years ago by ▴ 160 • written 7.8 years ago by ▴ 80
2
votes
1
reply
2.5k
views
How to add missing residues using swissPDBviewer
protein residues swissPDB
updated 4.5 years ago by ★ 30k • written 4.5 years ago by ▴ 10
0
votes
2
replies
1.5k
views
Computing multiple PRS on the fly with plink
prs plink
updated 4.5 years ago by 12k • written 4.5 years ago by • 0
1
vote
8
replies
3.8k
views
error in extracting one chromosome from multiple fasta files to a single fasta file
fasta
updated 4.5 years ago by 21k • written 4.5 years ago by • 0
0
votes
1
reply
1.2k
views
ATAC-seq fragment length distribution wrong but data makes sense!
atac-seq nucleosome
updated 4.5 years ago by 90k • written 4.5 years ago by ▴ 40
1
vote
3
replies
1.7k
views
Impute variants with the PHG. Pipeline and VCF final output for each sample
PHG
updated 4.5 years ago by 45k • written 4.6 years ago by ▴ 10
2
votes
5
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3.1k
views
How can I use log2 RPM data(RNA-seq) to find differentially expressed genes?
log2RPM RNA-seq
4.5 years ago by Tommmm • 0
1
vote
2
replies
1.1k
views
Batch correction on scRNA-Seq data
scRNA-Seq
4.5 years ago by elb ▴ 260
2
votes
3
replies
1.7k
views
Differential abundance analysis for bulk TCR-seq data
enrichment TCR differential DESEQ
4.5 years ago by pm2012 ▴ 140
0
votes
3
replies
1.9k
views
PLINK: ERROR: No nonmissing markers for individuals when using --cluster
vcf cluster genome treemix plink
updated 4.5 years ago by 11k • written 4.5 years ago by ▴ 10
1
vote
1
reply
1.3k
views
Gene Expression Deconvolution - Rationale/Logic
RNA-Seq gene expression deconvolution
updated 4.5 years ago by • 0 • written 5.9 years ago by ▴ 10
1
vote
5
replies
2.2k
views
EQTL FDR vs raw p-value
FUMA EQTL
updated 4.5 years ago by ★ 3.0k • written 4.5 years ago by ▴ 110
5
votes
4
replies
3.5k
views
Missing some output files for MultiQC
FastQC MultiQC RNA-Seq
4.5 years ago by courtney.e.hershberger ▴ 10
2
votes
4
replies
1.6k
views
vlookup function using awk for two vcf files?
vcf awk vlookup
4.5 years ago by Alexandros.Frydas ▴ 30
1
vote
1
reply
1.1k
views
heterozygosity
heterozygosity
updated 4.5 years ago by 2.9k • written 4.5 years ago by • 0
1
vote
1
reply
4.0k
views
scRNA-seq gene expressions from small number of cells
scRNA-seq gene expression cells
updated 4.5 years ago by ★ 19k • written 4.5 years ago by ▴ 140
0
votes
0
replies
766
views
News: Bayesian course using bmrs in R
statistics R Bayesian bmrs
4.5 years ago by Physalia-courses ★ 2.7k
0
votes
0
replies
526
views
NAs in p-value result of GWAS association analysis
GWAS
4.5 years ago by JFeng • 0
8
votes
4
replies
2.6k
views
What are important questions before starting analysis of 10x scRNA-seq dataset
10x scRNA-seq
updated 4.5 years ago by 154k • written 4.5 years ago by • 0
2
votes
3
replies
1.4k
views
Changing length of x axis on ggplot
r ggplot ggplot2
updated 4.5 years ago by ▴ 100 • written 4.5 years ago by ▴ 70
3
votes
1
reply
1.4k
views
VEP Disk Space
VEP Ensembl
updated 4.5 years ago by 24k • written 4.5 years ago by ▴ 110
5
votes
3
replies
2.5k
views
quantile normalization in deseq2
quantile_normailzation Deseq2 rna-seq
updated 4.5 years ago by 90k • written 4.5 years ago by ▴ 150
0
votes
0
replies
954
views
Job: Bioinformatician/Software Developer for Samplix R&D in Denmark
FluentEnglish LinuxEnvironment
updated 4.4 years ago by 45k • written 4.5 years ago by • 0
0
votes
1
reply
906
views
how to genrate fcgene pedinfo file
pedinfo impute2 fcgene
4.5 years ago by panmy2015 • 0
2
votes
3
replies
10k
views
cannot import name 'gcd' from 'fractions'
ubuntu Linux python multiqc
updated 4.5 years ago by ★ 1.5k • written 4.6 years ago by • 0
0
votes
3
replies
2.6k
views
Gerp++ installation error
gerp gerp++ SNP gerp2
updated 4.5 years ago by • 0 • written 6.8 years ago by ★ 1.2k
122,200 results • Page 660 of 2444
Recent Votes
strong appearing variant not found by haplotypecaller in -ERC mode and deepvariant but with haplotypecaller in normal mode
Answer: How can I easily remove overlapping transcripts, keeping only longest transcript
Answer: Log2 transformation is well used, but is there a good paper that can be used as
Answer: Flatten a GTF
Answer: RNA-seq - Creating SAF from NCBI gff for Subread featureCounts - keep 'gene' or
Can EdgeR of DeSeq be used for Single-cell RNA-seq?
Answer: Getting the overlap between two GTF files
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Recent Replies
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding by samuel.a.odonnell ▴ 640
I don't believe merqury ignores softmasked (lower case) nucleotides so I don't think that is the case. From what it sounds like, during th…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
Thanks a lot to be helpful I’m trying to build a complete `UniProtID` to `GeneSymbol` lookup table and I’m running into a wall. I’ve alrea…
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 20
thanks for the quick reply. i posted the screenshot. gatk-internally, there is still the difference using -ERC or not, priot is getting …
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 20
here the igv view. showing the histogram for all samples plus the reads for one: ![enter image description here][1] and expanded view of …
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
Check the read lengths to make sure the files are correct.
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by Pierre Lindenbaum 166k
> Any suggestions or help you could share please, show us an IGV screenshot of the position GATK realign the reads locally, discards read…
Comment: Can i use orthofinder for small protein datasets and not full proteome? by alexandrakortsi • 0
By sequence. Thank you for your response!
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding by xinguok794 ▴ 10
Thank you for your reply! Unfortunately, despite running YAHS with `--no-contig-ec`, the QV value of the resulting FASTA file did not impro…
Comment: Subsetting before QC in Spatial Transcriptomics by Kent ▴ 30
Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
Comment: Midpoint rooting IQTREE newick file moves node support around by Luca Arbore ▴ 10
Thank you very much Kevin, it worked!
Comment: ID unifiying across different datasets by GenoMax 154k
In this case the entry notes that this is likely the product of a pseudogene: https://www.uniprot.org/uniprotkb/Q5VTE0/entry and existence …
Comment: Comparison of different RNAseq data sets by DrSmad ▴ 10
Each lab contributes both control and LPS. Example, for cell line A_lab1 did and analysis on control and LPS-6h. Cell line B_lab2 did contr…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
sorry, why some gene names are often lacking though the Uniprot ID is still valid (using biomart)?
Comment: snpEff: Unsupported structural variant types by shpak.max ▴ 70
Unfortunately, while it ran without a problem initially, when I checked the run screen today, I saw the following error message (and unlike…
Comment: ID unifiying across different datasets by GenoMax 154k
You can use the [**ID mapping tool**][1] from UniProt site (third ID did not map from the list above): From To P68104 ENSG0000015…
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