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121,314 results • Page 427 of 2427
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4
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4
replies
1.5k
views
use gene symbol in heatmap instead of ensemble geneID
rnaseq heatmap
3.1 years ago by Claire • 0
0
votes
1
reply
606
views
Strange Per base sequence content of fastqc
fastqc scRNA-seq
updated 3.1 years ago by 151k • written 3.1 years ago by • 0
1
vote
2
replies
917
views
From .txt to .vcf
annotation vcf
updated 3.1 years ago by 166k • written 3.1 years ago by ▴ 60
0
votes
3
replies
2.1k
views
Trimming adaptors and primers for RNAseq reads
RNAseq cutadapt trimming
updated 3.1 years ago by ★ 7.6k • written 3.1 years ago by • 0
1
vote
4
replies
1.4k
views
Metagenomic quantification (abundance of reads on assembled reference)
viral-family viral-genus abundances metagenomic contigs
3.1 years ago by emiliomastriani ▴ 40
0
votes
0
replies
356
views
Exomiser - Unable to deserialise data
jannovar exomiser softwareerror
3.1 years ago by sammi • 0
0
votes
2
replies
1.7k
views
bcftools consensus overlapped variant
bcftools variant
updated 24 months ago by 45k • written 3.1 years ago by ▴ 60
3
votes
4
replies
1.1k
views
featureCounts results has many psedugenes(ENSG***) together with genes
featureCounts RNA-Seq
updated 3.1 years ago by 6.2k • written 3.1 years ago by ▴ 10
23
votes
12
replies
4.0k
views
Genes encoded on both strands of DNA?
Genes strand
updated 20 months ago by 45k • written 3.1 years ago by ▴ 170
0
votes
4
replies
952
views
Effect of gene expression level on CRISPR sgRNA library design
experssion Gene CRISPR
3.1 years ago by yanbinwan • 0
1
vote
2
replies
751
views
Create short fasta sequences from a vcf file.
bcftools WASP
updated 24 months ago by 45k • written 3.1 years ago by ▴ 10
1
vote
5
replies
1.3k
views
How to work with a BAM file that have an inaccessible reference genome
Genome fastq alignment Reference bam
3.1 years ago by Ak ▴ 60
0
votes
1
reply
1.0k
views
Filtering VCF variants based on txt file with variants CHROM, POS and ID
VCF
updated 3.1 years ago by 45k • written 3.1 years ago by ▴ 30
2
votes
1
reply
1.5k
views
[W::bgzf_read_block] EOF marker is absent in BBMAP
bbmap
updated 2.1 years ago by ▴ 10 • written 3.1 years ago by ▴ 20
0
votes
0
replies
451
views
Is CHASMplus appropriate for cancer cell-line data?
CHASMplus
3.1 years ago by songyeon0425 • 0
2
votes
2
replies
817
views
Building A Ultrametric Phylogenetic Tree With Integer Branch Length
ultrametric-tree
updated 3.1 years ago by 4.7k • written 3.1 years ago by ▴ 20
2
votes
1
reply
983
views
Get GO terms for list of NCBI genes from Gene Ontology API using Python
python gene-ontology
updated 3.1 years ago by ★ 1.6k • written 3.1 years ago by • 0
3
votes
5
replies
2.9k
views
Loading possorted_genome_bam.bam generated by 10X cellranger count command into IGV.
cellranger deeptools bigwig IGV single-cell
updated 24 months ago by 45k • written 3.1 years ago by ▴ 20
0
votes
0
replies
530
views
mirdeep2 - star sequence
mirdeep2
3.1 years ago by henry-keen ▴ 50
0
votes
0
replies
955
views
Making sense of Bandage graph after genome assembly
bandage flye assembly genome Nanopore
3.1 years ago by schulpen_91 ▴ 30
3
votes
1
reply
1.1k
views
What are the suggested parameters for running IQ-TREE on a protein alignment for phylogeny?
protein metagenomics phylogeny iqtree
updated 3.1 years ago by ★ 29k • written 3.1 years ago by ▴ 740
0
votes
0
replies
1.2k
views
how to visualize correctly significant splicing events- inconsistencies between rMATS results and IGV sashimi plots
splicing rMATS RNA-seq sashimi-plot STAR
3.1 years ago by Reuth • 0
2
votes
8
replies
4.3k
views
How to scale raw Counts to obtain z-score Heatmap in R?
GEO R
3.1 years ago by ali ▴ 20
2
votes
2
replies
1.0k
views
bowtie2 MAPQ scores more than 42
MAPQ bowtie2
3.1 years ago by rakusmaximus • 0
3
votes
3
replies
2.3k
views
Correlating DNA methylation beta values with Gene expression levels (RNA-seq)
correlation methylation DNA RNA-seq R
updated 3.0 years ago by 3.3k • written 3.1 years ago by ▴ 20
8
votes
8
replies
2.2k
views
Missing data per site
vcftools
updated 3.1 years ago by 2.9k • written 3.1 years ago by ▴ 20
4
votes
4
replies
3.2k
views
Latest dbSNP VCF
dbsnp
3.1 years ago by MAPK2 ▴ 50
1
vote
7
replies
3.5k
views
If R package is already install - load it; if not installed, install it
R
updated 3.1 years ago by 45k • written 3.1 years ago by ▴ 70
0
votes
0
replies
548
views
Correcting for Multiple Comparisons for Two-way ANOVA of Metabolomics Data
multiple ANOVA comparisons metabolomics
3.1 years ago by ylim33 • 0
2
votes
3
replies
1.7k
views
Best way to load all experiment samples into Seurat
GEO R
updated 3.1 years ago by 45k • written 3.1 years ago by • 0
0
votes
1
reply
1.4k
views
Job: Bioinformatics Developer/Trainer
developer trainer
updated 2.3 years ago by 45k • written 3.1 years ago by • 0
0
votes
1
reply
853
views
Job: Bioinformatics Scientists @ Leidos (Multiple positions, Atlanta GA USA/remote working)
Bioinformatics-scientist
updated 3.1 years ago by 45k • written 3.1 years ago by • 0
0
votes
3
replies
773
views
Labels in Enhanced Plot
enhanced labels plot r
updated 3.1 years ago by 45k • written 3.1 years ago by • 0
0
votes
1
reply
733
views
How to examine .hic files from Hi-C analysis?
Hi-C 3D-genome
updated 3.1 years ago by 151k • written 3.1 years ago by ▴ 40
3
votes
7
replies
4.8k
views
Varscan2 copynumber 'Parsing Exception' error
varscan2 samtools bam copynumber whole exome
updated 3.1 years ago by ▴ 30 • written 8.8 years ago by ▴ 50
0
votes
4
replies
1.2k
views
GDCquery - warning
maf GDCquery
3.1 years ago by Negatyvna • 0
0
votes
0
replies
415
views
Identifying multiple mappings with pd.clariom.d.human
biocounductor microarray
3.1 years ago by amir.rakhimov.b • 0
5
votes
6
replies
4.8k
views
6 follow
Split Vcf File Using Gatk
genome gatk vcf parsing
updated 3.1 years ago by • 0 • written 13.0 years ago by ▴ 850
0
votes
0
replies
450
views
Normalize different chromatin accessibility methods to make them comparable
peakcalling scaling ATAC_seq Normalisation heatmap
updated 3.1 years ago by 45k • written 3.1 years ago by • 0
2
votes
1
reply
719
views
How to define a column class in R, dataframe
colclasses R dataframe
3.1 years ago by mthm ▴ 80
0
votes
2
replies
699
views
Extract 3'utr sequences from annotation file
rstudio bam
updated 2.2 years ago by 45k • written 3.1 years ago by • 0
0
votes
4
replies
965
views
Designing unique DNA sequence set
sequence-specific
updated 3.1 years ago by 45k • written 3.1 years ago by ▴ 10
0
votes
0
replies
955
views
Job: Full-Time Computational Biologist / Bioinformatics Scientist - Baltimore (USA) | Fredericton (Canada) | Remote
python R ML programming
updated 3.1 years ago by 45k • written 3.1 years ago by • 0
0
votes
0
replies
580
views
Job: Postdoctoral research scholar position in bioinformatics/data science at the University of Iowa
postdoctoral data-science
updated 3.1 years ago by 45k • written 3.1 years ago by • 0
1
vote
1
reply
728
views
Reasonable number of mutations in a human cancer cell exome
exome
updated 3.1 years ago by 4.7k • written 3.1 years ago by • 0
0
votes
1
reply
2.0k
views
Job: Programmer or Software Developer in Bioinformatics
genomics algorithms DNA-sequencing programming
updated 3.1 years ago by 21k • written 3.1 years ago by • 0
1
vote
0
replies
712
views
News: Phase 1 of the NCTR Indel Calling from Oncopanel Sequencing Data Challenge is now live!
oncopanel indel-calling
updated 2.5 years ago by 45k • written 3.1 years ago by ▴ 10
4
votes
5
replies
4.3k
views
How to manage memory contraints when analyzing a large number of gene count matrices? I keep running out of RAM with my current pipeline.
matrix scRNA-seq RNA Seurat memory
updated 3.1 years ago by 88k • written 3.1 years ago by ▴ 30
9
votes
4
replies
1.2k
views
RNA-Seq with more conditions
conditions validation RNA-Seq
updated 3.1 years ago by 11k • written 3.1 years ago by • 0
1
vote
2
replies
830
views
defuse installation
installation defuse
updated 3.1 years ago by ★ 1.9k • written 3.1 years ago by ▴ 60
121,314 results • Page 427 of 2427
Recent Votes
Finding the significance of the overlap between 2 or more gene sets using simulation in R.
Finding the significance of the overlap between 2 or more gene sets using simulation in R.
Comment: How to add GFP in STAR reference?
nanopore unaligned bam files
WGCNA Soft Power Problem
Choosing a high soft thresholding power in WGCNA, is it reasonable?
A: Extracting certain columns from VCF file
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Recent Replies
Comment: IGV view for Chromatin accessibility ATAC-seq by ATpoint 88k
How were these tracks generated? Is it bigwig files (or bedGraphs) at single-base resolution or was it like deeptools bamCoverage which by …
Answer: Using VEP custom input by Pierre Lindenbaum 166k
> VEP can integrate custom annotation from standard format files into your results by using the --custom flag. see https://www.ensem…
Comment: WGCNA pickSoftThreshold problem by ton_of_questions • 0
Thank you for your reply! Although I don't really understand how to use hard Threshold. I plotted raw correlations and kept the most correl…
Comment: Phased haplotype using WGS data from Nebula Genomics and GATK by colindaven 7.6k
You'll need to align the reads using a tool like `bwa mem` first. Try doing a tutorial to get the concepts or read through at least some of…
Answer: Phased haplotype using WGS data from Nebula Genomics and GATK by biostars ▴ 30
I believe I found the correct reference genome for the odd man out. It is hg38 which seems like one of the original older reference genomes…
Answer: How to interpret Nucleosome banding pattern in scATAC-Seq? by Jan • 0
Hey, seems like his account is not existing anymore. If anyone else is still interested, I developed a tool evaluating the nucleosomal s…
Comment: How to add GFP in STAR reference? by GenoMax 151k
It may be best to include a `gene` entry in addition so the file matches [**GTF spec**][1]. GFP unknown gene 1 580 . …
Comment: Cut&Run TF Analysis - Very Low Peak Counts Despite Good Library Quality by jared.andrews07 ★ 18k
The low number of peaks called is your confirmation. You've visually confirmed there's no real issue with peak calling in your data - there…
Comment: How to add GFP in STAR reference? by lieven.sterck 15k
Not even I think, it will just report that reads were counted in the opposite strand, but do check 'cus if you do really stringent counting…
Comment: How to add GFP in STAR reference? by bioinfo ▴ 160
Thank you. If I put the wrong stand will I just not get any counts for GFP?
Answer: WGCNA blockwiseModules function for small datasets by LChart 5.0k
You lose some granular control over parameters. If you set the block to be larger than the number of genes, you just get a "default" run of…
Comment: How to add GFP in STAR reference? by lieven.sterck 15k
Not a strict requirement as far as I remember, I think it will even except a . (dot) for the strand (== unstranded feature) I would assum…
Comment: Cut&Run TF Analysis - Very Low Peak Counts Despite Good Library Quality by sk ▴ 20
Is there any other way to confirm this (quantitatively)? I am trying to conclude this analyses/see if I can find useful information.
Comment: Understanding STARsolo --soloStrand values and 10X scRNA-seq library structure by dsull ★ 7.6k
You would use clip5pNbases (because you're clipping from the 5' end [i.e. the left-side] of the R1 read). You would use Reverse, because t…
Answer: Can you compare GETx and TCGA miRNA non normalized counts a by ATpoint 88k
This was asked dozens of times before, please searh for previous threads. In brief, batch is nested with condition, so actually it's not po…
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