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122,012 results • Page 605 of 2441
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2
votes
2
replies
1.5k
views
Will this de novo transcriptome assembly be useful in looking at RNAseq differential expression?
de-novo-assembly
updated 2.0 years ago by 45k • written 4.2 years ago by ▴ 170
2
votes
3
replies
1.4k
views
Exonerate - using it in another project
Exonerate
updated 4.2 years ago by ★ 2.9k • written 4.2 years ago by • 0
0
votes
1
reply
855
views
How to caclulate polarity
python polarity AA
updated 4.2 years ago by 22k • written 4.2 years ago by • 0
0
votes
0
replies
1.1k
views
What is the difference between Protein-protein interactions (eg: PPI network from STRING database) network and protein functional interaction network…
interaction protein analysis ontology ReactomeFiviz database network protein-protein gene String
4.2 years ago by anandprem1792 ▴ 60
0
votes
3
replies
2.4k
views
How can I find matches between two csv files according to multiple columns using awk/bash?
awk genomics bash
updated 4.0 years ago by 5.9k • written 4.2 years ago by • 0
0
votes
0
replies
1.2k
views
configparser.NoOptionError: No option 'gene_regions' in section: 'mm10' : when use rgt-hint footprinting
ATAC-seq footprinting
4.2 years ago by 17318598206 ▴ 30
0
votes
0
replies
601
views
Is it possible to compare signals from separate BeadChips?
Illumina batch-effect BeadChips
updated 13 months ago by 45k • written 4.2 years ago by • 0
1
vote
3
replies
2.4k
views
No INFO/info value in headers
VCF Michigan-Imputation-Server
updated 4.2 years ago by 45k • written 4.2 years ago by • 0
1
vote
4
replies
2.5k
views
How do you add gene annotations from a Diamond Blastx tsv file to a csv file with RNAseq differential expression data?
BLASTx RNA-seq diamond
updated 2.0 years ago by 45k • written 4.2 years ago by ▴ 170
0
votes
0
replies
614
views
STAR aligner output report gives %2 uniquely aligned reads while
RNA-Seq HERV
4.2 years ago by mb86 • 0
0
votes
2
replies
2.1k
views
understanding snpEff/snpSift concordance output
snpEff snpSift SNP concordance
updated 4.2 years ago by • 0 • written 5.5 years ago by • 0
2
votes
1
reply
3.3k
views
results from SNPSift Concordance
SNPSift concordance snp
updated 4.2 years ago by • 0 • written 8.5 years ago by ▴ 390
0
votes
1
reply
1.1k
views
Job: Automation Engineer
Engineer
updated 4.2 years ago by 45k • written 4.2 years ago by ▴ 70
0
votes
6
replies
7.4k
views
featureCounts parameters for RNA-Seq
featurecounts RNA-Seq Subread ReadCounts
updated 4.2 years ago by • 0 • written 5.8 years ago by ▴ 50
0
votes
0
replies
725
views
RNAseq only paired ends reads using featurecounts, should I pay attention to count only reads match to one strand?
rna featurecounts paired
4.2 years ago by wang-yanfang • 0
0
votes
2
replies
1.3k
views
Best way to evaluate the relationship between protein and RNA abundance
RNA protein
4.2 years ago by haasroni • 0
0
votes
0
replies
695
views
is it possible to subset samples and reheader a vcf in a single step?
bcftools
4.2 years ago by curious ▴ 900
0
votes
2
replies
1.5k
views
How to obtain subpopulation specific allelic variants from a .vcf file using PLINK?
1000genomes vcf plink
updated 2.6 years ago by 45k • written 4.4 years ago by • 0
2
votes
3
replies
1.7k
views
Cuffmerge running time
Cuffmerge
updated 4.2 years ago by ★ 1.1k • written 4.2 years ago by ▴ 50
2
votes
5
replies
1.8k
views
Same strand, same QNAME different FLAG?
strand featureCounts SAM RNAseq
4.2 years ago by compuTE ▴ 140
0
votes
0
replies
1.1k
views
Cut-off value from qvalue package R for Manhattan plot
GWAS qvalue threshold significant plot manhattan rrBLUP
4.2 years ago by b.g.tamang ▴ 20
5
votes
8
replies
3.4k
views
Strand specific quantification with strand-splitted BAM files
featureCounts SAM strand RNAseq
updated 4.2 years ago by 103k • written 4.2 years ago by ▴ 140
0
votes
2
replies
1.0k
views
Combine haploid fastq's into diploid "individuals"
GATK pop-gen haplodiploid
4.2 years ago by timothy.delory ▴ 20
0
votes
0
replies
914
views
ABSOLUTE calls on CCLE cell-lines
Allele-specific LOH CNV ABSOLUTE CCLE
4.2 years ago by Nisha • 0
1
vote
2
replies
1.9k
views
How to download this genome?
genome
updated 4.2 years ago by 154k • written 4.2 years ago by ▴ 30
1
vote
2
replies
1.3k
views
Collect ITS sequences from bacterial genomes
rRNA ITS internal 16S transcribed taxonomy region
updated 4.2 years ago by ★ 30k • written 4.2 years ago by ▴ 50
0
votes
0
replies
619
views
Calculating frequencies for first-order Markov model given G+C content and CpG fraction
Markov model
4.2 years ago by valba • 0
4
votes
6
replies
1.9k
views
Differentially gene expression multispecies
Expression Multispecies Rnaseq differentially
updated 2.7 years ago by ▴ 40 • written 4.2 years ago by ▴ 40
2
votes
4
replies
7.2k
views
Going from Seurat object to DESeq2 analysis
DEG single-cell DESeq2 scRNAseq Seurat
updated 4.2 years ago by 4.2k • written 4.2 years ago by ▴ 50
2
votes
3
replies
1.5k
views
No out put from python function
Python
4.2 years ago by ThulasiS ▴ 90
4
votes
6
replies
3.1k
views
Measuring pairwise distances between residues/atoms in structural alignment of protein family
biopython protein alignment distance pairwise
updated 4.2 years ago by 22k • written 4.2 years ago by ▴ 70
0
votes
0
replies
845
views
VCFtools giving me a blank output for Tajima's D test at certain loci
Tajima population neutrality
4.2 years ago by milesandersonmn ▴ 20
0
votes
0
replies
587
views
Do you know a sofware to draw pedigrees + haplotypes?
mutation Haplotype pedigree Cyrilic sequencing
4.2 years ago by Negar • 0
1
vote
3
replies
5.4k
views
How to use 1000 Genomes data for LDheatmap package in R
SNP R lingkage ldheatmap heatmap
updated 4.2 years ago by ▴ 20 • written 9.9 years ago by ▴ 10
1
vote
4
replies
1.3k
views
aGPCR
GPCR
4.2 years ago by keyajoshi1996 • 0
0
votes
0
replies
529
views
Secondary structure information using cpptraj
CPPTRAJ
4.2 years ago by keyajoshi1996 • 0
3
votes
6
replies
2.8k
views
BWA MEM fail to open file for output SAM
sam index bwa output
updated 4.2 years ago by 89k • written 4.2 years ago by ▴ 60
6
votes
7
replies
5.3k
views
Biopython SeqIO: AttributeError: 'str' object has no attribute 'id'
filtering biopython fasta python sequence
updated 4.2 years ago by ★ 1.6k • written 4.2 years ago by ▴ 10
0
votes
2
replies
1.2k
views
Plot assigned / unassigned reads distance to 3'UTR
bedtools RNA-seq closest
4.2 years ago by nlehmann ▴ 150
2
votes
4
replies
2.4k
views
How to compare LD of a gene for all subpopulations in 1000 Genome?
LDPlot SNPs variants 1000Genome
4.2 years ago by Rashmi ▴ 20
3
votes
11
replies
7.5k
views
Converting gene symbols to protein (uniprot) ids gives multiple matches per gene symbol. Why?
Uniprot r
updated 4.2 years ago by 21k • written 4.2 years ago by ▴ 60
0
votes
0
replies
1.1k
views
manhattan plot
fst vcf manhattan
4.2 years ago by anithanagaraj93 ▴ 10
4
votes
6
replies
1.8k
views
Genome analysis and improvement
genome
4.2 years ago by Duminda ▴ 10
0
votes
4
replies
3.2k
views
How to modify dot plot in MUMmer 3 for bacteria comparative genomics?
mummerplot
updated 4.2 years ago by ★ 30k • written 4.2 years ago by ▴ 30
4
votes
4
replies
1.7k
views
Exonerate - issues when running it
Exonerate
4.2 years ago by helloword • 0
0
votes
1
reply
813
views
Using FPKM value from the database
gene-expression FPKM
updated 4.2 years ago by 45k • written 4.2 years ago by ▴ 40
0
votes
5
replies
3.7k
views
CellPhoneDB results
CellPhoneDB statistics
4.2 years ago by torabian.p • 0
0
votes
0
replies
707
views
How can I find genomes that have linked transcriptome data ? (bacteria)
bacteria esearch ncbi
4.2 years ago by hugo.avila ▴ 540
4
votes
4
replies
2.1k
views
Extract subject sequences from Blast result
sequence blast homology
4.2 years ago by mnsp088 ▴ 100
0
votes
0
replies
754
views
GSEA p value dependent on pre-ranked list size?
gsea enrichment p-value statistics
4.2 years ago by garfield320 ▴ 20
122,012 results • Page 605 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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