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122,012 results • Page 290 of 2441
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594
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fold stability
fold rna segment stability
updated 2.6 years ago by 154k • written 2.6 years ago by ▴ 20
0
votes
1
reply
1.1k
views
Why 0/0 genotype refers to SNP and ALT != REF (in vcf file after freebayes)
genotype vcf freebayes SNP vcflib
2.6 years ago by poecile.pal ▴ 50
3
votes
4
replies
2.0k
views
What is the general structure of a WDL that implements "embarrassing parallelization"?
wdl cromwell
updated 2.6 years ago by 5.1k • written 2.6 years ago by ▴ 70
0
votes
2
replies
1.1k
views
HISAT2
aligner HISAT2
updated 2.6 years ago by 89k • written 2.6 years ago by • 0
2
votes
4
replies
1.8k
views
Trouble with transcripts_id when using how_are_we_stranded_here python package
bash sequencing RNA-seq
2.6 years ago by ExtentHonest56 ▴ 30
12
votes
7
replies
2.6k
views
6 follow
how to edit fasta header
fasta
updated 2.6 years ago by 12k • written 2.6 years ago by • 0
3
votes
7
replies
2.9k
views
Does running samtools sort in parallel result in unexpected output due to temporary file conflicts?
NGS samtools bam
updated 2.3 years ago by 45k • written 2.6 years ago by ▴ 120
0
votes
0
replies
692
views
Calculating Ne (effective population size) for big data
data Ne big
2.6 years ago by Star:) ▴ 50
2
votes
1
reply
1.0k
views
Genetic risk score calculated using SNPs with mixed effect directions
polygenic risk score genetic
updated 2.6 years ago by ★ 4.8k • written 2.6 years ago by ▴ 40
0
votes
0
replies
667
views
CalcPerturbSig() Seurat
scRNA-seq single-cell differential-expression Seurat
updated 23 months ago by 45k • written 2.6 years ago by • 0
2
votes
8
replies
2.5k
views
How to remove duplicate and reverse duplicate hits from BLASTn results?
bash-scripting gene R BLAST
2.6 years ago by anikcropscience ▴ 270
6
votes
7
replies
2.6k
views
Transcript vs primary transcript on phytozome.
primary transcripts phytozome
updated 2.6 years ago by 103k • written 2.6 years ago by ▴ 10
0
votes
2
replies
1.9k
views
Trying to make a Mauve alignment with 2 sequences and keep getting error code 3
alignment Mauve gene DNA
updated 2.6 years ago by ▴ 20 • written 2.6 years ago by • 0
3
votes
8
replies
2.3k
views
Which gatk version generates VCF version 4.1
vcf_v4.1 gatk
2.6 years ago by taniamahmood38 ▴ 60
0
votes
0
replies
628
views
How to analyze SCRNA seq data labelled with LARRY?
single lineage RNA tracing LARRY
updated 2.6 years ago by 154k • written 2.6 years ago by ▴ 160
0
votes
1
reply
857
views
WGS sample has lower mapping rate (92%), bimodal depth of coverage peak and aberrant synonymous/missense variation rate
WGS whole sequencing genome
updated 2.6 years ago by ★ 3.0k • written 2.6 years ago by • 0
2
votes
2
replies
901
views
fastq file for GSE151671
fastq
2.6 years ago by Andy ▴ 120
2
votes
1
reply
1.0k
views
N50 value is equal to the single contig?
N50
updated 2.6 years ago by 48k • written 2.6 years ago by ▴ 50
13
votes
4
replies
5.0k
views
long read + salmon? (transcript abundance)
long-read salmon
updated 18 months ago by 45k • written 2.6 years ago by ▴ 60
0
votes
0
replies
617
views
Exception in thread "main" java.lang.NoClassDefFoundError: Could not initialize class java.io.FilePermission
PICARD
2.6 years ago by Hayler Edu ▴ 40
1
vote
0
replies
836
views
News: Virtual Single Cell RNA-seq Workshop
single genomics cell expression rna-seq workshop gene
2.6 years ago by mia.nahom ▴ 10
3
votes
3
replies
1.7k
views
Using vcfR to group variants per annotations
vcf vcfR R
updated 2.6 years ago by ★ 3.1k • written 2.6 years ago by ▴ 210
0
votes
0
replies
644
views
Question about ChIPseeker parameters
ChIP-seq ChIPseeker R
2.6 years ago by Jen ▴ 100
3
votes
11
replies
5.0k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
RNAseq cluster-profiler KEGG GSEA
2.6 years ago by redafazazi ▴ 30
1
vote
2
replies
696
views
Getting Refseq ids from Protein IDs
assembly
2.6 years ago by Amogh • 0
1
vote
2
replies
1.2k
views
Multinomial Distributions for large n
math multinomial distribution bayesian statistics
2.6 years ago by rtrende ▴ 80
0
votes
0
replies
760
views
Tools for identifying trans-splicing from long read data
long-read splicing nanopore trans-splicing
updated 18 months ago by 45k • written 2.6 years ago by ★ 3.1k
0
votes
0
replies
548
views
Aligning single transcript to sequence
Annotation alignment genome pseudogene sequence
2.6 years ago by bram_danneels • 0
0
votes
0
replies
666
views
Merge replicates for CHIP-seq analysis
Chip-seq
2.6 years ago by michelafrancesconi9 ▴ 20
0
votes
0
replies
560
views
Retrieving connected genes from KEGG pathways
data KEGG
2.6 years ago by Jaehyun ▴ 10
0
votes
0
replies
666
views
Customize colors in aheatmap() function from NMF package in R
heatmap NMF R
2.6 years ago by David R ▴ 20
0
votes
1
reply
988
views
Bwa mem different alignment results for the same reference genome
BWA-mem
updated 2.6 years ago by ★ 3.0k • written 2.6 years ago by • 0
0
votes
1
reply
1.1k
views
Will filter cell by highly variable genes (HVG) selection marks DGE for the filtered out low variable genes in further analysis?
HVG scSeq DGE
updated 2.6 years ago by 89k • written 2.6 years ago by • 0
0
votes
0
replies
692
views
Almost no peak output after peakcalling of mtDNA with MACS2
mtDNA python chip-seq MACS2
updated 2.6 years ago by 45k • written 2.6 years ago by • 0
2
votes
1
reply
844
views
fastQC - how to know if sample is good quality ?
fastqc
updated 2.6 years ago by 45k • written 2.6 years ago by ▴ 140
2
votes
2
replies
1.8k
views
Salmon lib_format_counts.json - explanation
RNAseq strand-specificity transcriptomic Salmon
2.6 years ago by Lada ▴ 40
0
votes
1
reply
920
views
Help with metatranscriptomics: makeContrasts design and checking for housekeeping gene expression levels?
metatranscriptomes RNA-seq Trinity
updated 2.6 years ago by 45k • written 2.6 years ago by ▴ 10
0
votes
5
replies
1.9k
views
ANOVA results viz from ssGSEA
visualization ssGSEA anova
updated 2.6 years ago by 5.1k • written 2.6 years ago by ▴ 20
6
votes
1
reply
1.2k
views
Plotting 3 Y axis vs x
r ggplot2
updated 2.6 years ago by 5.1k • written 2.6 years ago by ▴ 860
1
vote
2
replies
1.4k
views
Enrichment analysis based on kegg for zebrafish
KEGG enrichment ClusterProfiler R
2.6 years ago by PBC ▴ 10
0
votes
0
replies
483
views
Add or Simulate Noise in Short-Read Paired End Data
pair short-read spurious discordant
2.6 years ago by Suraj • 0
3
votes
9
replies
7.1k
views
Batch effect in integrated RNA-seq analysis
batch-effect RNA-seq Combat
updated 2.6 years ago by 5.1k • written 2.6 years ago by • 0
1
vote
0
replies
666
views
News: Advanced Bayesian statistics in R course
Statistics RegressionModeling Bayesian R
2.6 years ago by Physalia-courses ★ 2.7k
0
votes
2
replies
2.3k
views
Problem with universe argument in enrichKEGG
enrichment KEGG clusterProfiler
2.6 years ago by 1215045934 ▴ 80
2
votes
4
replies
1.7k
views
PHG Load haplotype and create consensus
haplotype Consensus PHG
updated 2.6 years ago by ▴ 420 • written 2.7 years ago by ▴ 20
0
votes
0
replies
988
views
Job: Postdoctoral Fellow – Computational Biology (Genetic Interactions in Cancer)
networks cancer crispr postdoc
2.6 years ago by Colm • 0
9
votes
6
replies
2.0k
views
how to download 3' UTR sequences of Anas platyrhynchos?
miRNA gene target-prediction
updated 2.6 years ago by 154k • written 2.6 years ago by ▴ 30
1
vote
0
replies
631
views
How to get a partition file for phylogenetic trees?
phylogenetic python analysis partition
2.6 years ago by YOUSEUFS ▴ 30
0
votes
4
replies
1.6k
views
Combine VCF files
vcf bcftools
updated 2.6 years ago by 103k • written 2.6 years ago by ▴ 70
11
votes
17
replies
7.0k
views
How do one analyze data from SMART-Seq stranded kit (v4)?
single-cell smart-seq
updated 2.6 years ago by ★ 7.7k • written 2.6 years ago by ★ 1.9k
122,012 results • Page 290 of 2441
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Recent Replies
Comment: hisat2 error-Paired end reads not equal or lack of RAM/disk space? by lieven.sterck 16k
ok, missed that ... in any case that should not happen indeed. How did you determine that the files are not equal? I can indeed also see t…
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Ram 45k
Do you have a plan to make an English version of the UI?
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Edward • 0
This can visualize the parameters of the generated workflow, software, and scripts, and manage the docker process of the script, software, …
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by ATpoint 89k
Can you summarize in one sentence what the use case is? Is this a workflow manager?
Comment: Pseudogene - scarce info by ATpoint 89k
This reminds me strongly on my "masters" courses (doesn't deserve that name tbf). "Here is some poorly-described project with little to no …
Answer: scVI vs Harmony, which is better for cell type based clustering in brain tissue? by ATpoint 89k
There is no "better" is my experience. It always depends on the dataset. Try both and integrate your biological knowledge to decide which m…
Comment: DESeq2 on metagenome KO counts by Aleksandra ▴ 180
I just wrote that I misunderstood your initial question.
Comment: DESeq2 on metagenome KO counts by Aleksandra ▴ 180
What exactly did I not get?
Comment: Interpreting genomic features distribution for CUT&RUN peaks by rfran010 ★ 1.7k
If I understand correctly, you see increased signal at TSS sites compared to control (taller peaks in browser). However, 92% of the 450 siS…
Comment: combine VCF from diploid reference/haplotypes for the same sample by cmdcolin ★ 4.3k
this question is a little similar to your previous question (https://www.biostars.org/p/9614638/). just as added info, here is a tool calle…
Comment: hisat2 error-Paired end reads not equal or lack of RAM/disk space? by aj123 ▴ 130
As mentioned above, I just got the raw fastq files from the ftp site listed.
Comment: DESeq2 on metagenome KO counts by ATpoint 89k
This statement makes zero sense in response to what I wrote.
Comment: DESeq2 on metagenome KO counts by Aleksandra ▴ 180
I focused on the fact that DESeq2 models overdispersion, but overlooked its implicit assumption: normalisation works when the main source o…
Comment: DESeq2 on metagenome KO counts by Aleksandra ▴ 180
Thank you very much. I mistakenly drew a superficial analogy. I equated KO counters with gene counters.
Comment: DESeq2 on metagenome KO counts by ATpoint 89k
Both vst or logcpm will favor expression level (magnitude of counts) rather than differences in a hclust/heatmap. For differences you need …
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