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Job: at Mogrify: Bioinformatician
NGS AlgorithmDev R Python SingleCellSequencing
4.5 years ago by Mogrify Talent Acquisition ▴ 10
2
votes
2
replies
1.9k
views
Bedtools intersect 0- and 1-based coordinate files
gff intersect bedtools bam
4.5 years ago by maxrwjones ▴ 60
0
votes
1
reply
925
views
How to extract translated sequence of pol gene from a GenBank file
gene genbank genome sequence biopython
updated 4.5 years ago by 154k • written 4.5 years ago by • 0
1
vote
5
replies
2.8k
views
Liftover vcf file from hs37d5 assembly to b37 assembly
vcf liftover assembly
updated 4.2 years ago by ▴ 110 • written 4.5 years ago by ▴ 420
15
votes
7
replies
12k
views
7 follow
Negative Fst values in Lositan
SNP Fst Lositan
updated 7 months ago by ▴ 330 • written 10.8 years ago by ▴ 60
0
votes
3
replies
1.4k
views
Issue on downloading fastPHASE in Mac
fastPHASE
updated 4.5 years ago by 2.9k • written 5.3 years ago by ▴ 90
1
vote
2
replies
1.8k
views
How can I convert .ali file to FASTA format?
fasta ali
updated 2.7 years ago by 45k • written 4.5 years ago by ▴ 50
0
votes
0
replies
779
views
Classifying microbial community as pathogen, opportunistic pathogen, nonpathogen?
Microbes Classification
4.5 years ago by MSRS ▴ 590
0
votes
0
replies
734
views
Create gtf annotations to a fasta file, based on a similar known genome.
sequencing annotations fasta gtf
4.5 years ago by adi.rotem ▴ 20
0
votes
2
replies
1.2k
views
SNP Analysis
WGS bacteria SNP phenotype
2.9 years ago by ghs101 • 0
0
votes
3
replies
4.1k
views
RNA seq V2 mRNA calculation information from cBioportal
RNA-Seq
updated 4.5 years ago by 45k • written 7.2 years ago by ▴ 30
2
votes
8
replies
5.5k
views
RNA Seq V2 RSEM Data
RNA-Seq
updated 4.5 years ago by ★ 1.3k • written 6.4 years ago by • 0
0
votes
0
replies
750
views
Nucleotide Frequency - HOMER?
HOMER
4.5 years ago by kstangline ▴ 110
1
vote
1
reply
1.3k
views
Pindel Config File Error
software error
updated 4.5 years ago by • 0 • written 6.7 years ago by ▴ 10
1
vote
4
replies
1.7k
views
T-test analysis for gene expression comparison
RNA-seq
updated 4.5 years ago by ▴ 840 • written 4.5 years ago by ▴ 10
3
votes
5
replies
2.0k
views
Single cell analysis
TCGA R singlecellanalysis scRNAseq
4.5 years ago by leticia ▴ 20
8
votes
13
replies
3.9k
views
Snakemake and STARsolo
scRNA-seq snakemake Mapping STARsolo
updated 4.5 years ago by 45k • written 4.5 years ago by ▴ 10
4
votes
3
replies
4.1k
views
How to plot the heat map of a subset of cell types using plotHeatmap from scater package
scRNAseq scRNA SingleR plotHeatmap scater
4.5 years ago by FantasticAI ▴ 60
0
votes
0
replies
736
views
Querying the Pathway Commons API returns empty string
Interactions API Pathway Database Commons
4.5 years ago by abel_jansma • 0
2
votes
2
replies
1.2k
views
Bacterial Seq Alignment
Alignment Sequencing Bacteria
4.5 years ago by ravihansa82 ▴ 130
0
votes
0
replies
1.0k
views
Job: Opportunity: Bioinformatics Engineer - Bioinformatics Core @ Memorial Sloan Kettering Cancer Center, New York, NY (US)
cancer_biology Python R
updated 4.4 years ago by 45k • written 4.5 years ago by ▴ 10
4
votes
3
replies
3.4k
views
ERROR: Reference and target files have no markers in common in interval: 6:63979-21294564
beagle imputation
updated 4.5 years ago by ▴ 10 • written 5.3 years ago by ▴ 30
5
votes
7
replies
4.1k
views
Error in running miRDeep2
Whitespace miRDeep2 error
updated 2.9 years ago by 45k • written 4.6 years ago by • 0
0
votes
0
replies
1.4k
views
Remove cells from Seurat object based on gene expression of makers
rnaseq singlecell seurat scrna
4.5 years ago by ahmad mousavi ▴ 800
0
votes
0
replies
724
views
Difference in SNP number in the output of Poolfreqdiff and Popoolation2 using the same filters.
pool-seq
4.5 years ago by AGE ▴ 30
3
votes
5
replies
3.9k
views
Can someone help me install ambertools on mac OS?
Installation MacOS amber ambertools
updated 4.5 years ago by 90k • written 4.5 years ago by ▴ 10
1
vote
5
replies
3.4k
views
How do I filter a multi-individual BCF file for genotype probabilities
vcf bcf
2.9 years ago by devenvyas ▴ 770
1
vote
2
replies
3.0k
views
Merge Gene expression and Antibody capture data in Seurat
10x seurat
4.5 years ago by chi.delta ▴ 40
1
vote
1
reply
1.8k
views
Hypothetical protein from Prokka and mapping them on KEGG
kegg blastkoala hypothetical protein prokka
updated 4.5 years ago by ★ 30k • written 4.5 years ago by ▴ 70
0
votes
0
replies
894
views
EdgeR Alternative Splicing
RNA-seq EdgeR
4.5 years ago by wei.zhang • 0
0
votes
0
replies
1.1k
views
limma: extracting coefficients and design matrix?
limma glm
updated 4.5 years ago by 21k • written 4.5 years ago by ▴ 220
1
vote
3
replies
2.8k
views
limma: extracting coefficients for complex models
limma r
4.5 years ago by fr ▴ 220
2
votes
3
replies
1.2k
views
Transcriptome mapping without reference.
Transcriptome Rna-seq Expression Differential
4.5 years ago by tiagobellintani ▴ 40
2
votes
4
replies
2.9k
views
Merge 2 GTF using agat avoiding overlapping
Merge GTF GFF agat
updated 4.5 years ago by 9.3k • written 4.5 years ago by ★ 1.3k
1
vote
1
reply
1.5k
views
Problem with universe values for GO categories in EnrichGO
EnrichGO clusterProfile
updated 4.5 years ago by ★ 3.1k • written 4.5 years ago by • 0
1
vote
6
replies
2.6k
views
Warning messages: In svgStyleAttributes(style, svgdev) : Removing non-SVG style attribute name(s): subscripts, group.number, group.value
rstudio r arrayexpress microarray
updated 4.5 years ago by 2.9k • written 4.5 years ago by ▴ 20
0
votes
0
replies
699
views
Is there an existing function which averages gene expression across cells which I wish to pool?
scRNA-seq singlecellRNAseq RNA-Seq scRNAseq
4.5 years ago by Sanjay • 0
2
votes
8
replies
3.5k
views
How to extract translated sequence of a partcular gene by parsing GenBank file
gene GenBank genome Biopython sequence
updated 4.5 years ago by 21k • written 4.5 years ago by • 0
7
votes
6
replies
8.3k
views
6 follow
GSEA with mouse RNAseq data
RNA-Seq
updated 4.5 years ago by ★ 8.6k • written 6.7 years ago by ▴ 90
1
vote
1
reply
1.4k
views
Enrichment of a specific GO term
rnaseq clusterprofiler
updated 4.5 years ago by ★ 90k • written 4.5 years ago by ▴ 20
10
votes
19
replies
6.0k
views
What is a difference between uniprot and 'nr. Non-redundant GenBank...'?
Genebank blast UniProt
updated 4.5 years ago by 154k • written 4.5 years ago by ▴ 20
7
votes
3
replies
1.6k
views
Why my files ended with ^M ?? (shell/bash)
shell linux cat grep bash
4.5 years ago by nlt_220593 ▴ 20
1
vote
1
reply
2.8k
views
LD matrix in PLINK
matrix plink ld
4.5 years ago by nlt_220593 ▴ 20
0
votes
4
replies
2.6k
views
No space separating sequence and name PopArt error !?
popart traits haplotypes python
updated 2.5 years ago by 45k • written 4.5 years ago by • 0
1
vote
2
replies
1.3k
views
How to merge and compare multiple bed files containg some overlaps?
awk genome Bedtools Bed
updated 2.7 years ago by 45k • written 4.5 years ago by ▴ 140
0
votes
1
reply
1.6k
views
Error in the "autoNoise0" stage while doing de novo assembly of Bionano data
BioNano Assembly
updated 4.5 years ago by • 0 • written 6.5 years ago by • 0
3
votes
5
replies
2.9k
views
6 follow
How to visualise differential expression analysis
expression Differential RNAseq
updated 4.5 years ago by 15k • written 4.5 years ago by • 0
5
votes
5
replies
2.3k
views
boxplot using ggplot2 in R
R boxplot ggplot2
updated 4.5 years ago by 21k • written 4.5 years ago by ▴ 20
0
votes
0
replies
684
views
Re-docking with the co-crystallized ligand showing +ve binding energy in Autodock4
re-docking protein docking
4.5 years ago by doubtbio • 0
0
votes
0
replies
865
views
ANOVA for eliminating genes with low variance for scRNASeq data
scrnaseq pca variance anova
updated 4.5 years ago by 90k • written 4.5 years ago by ▴ 30
122,200 results • Page 659 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: 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…
Answer: The geo samples is not having sentrix id and sentrix position. But this informat by yura.grabovska ▴ 890
Crosspost from related question: https://www.biostars.org/p/9616466/#9616534 ``` ##Using R, illuminaio from Bioconductor library(…
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