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122,020 results • Page 304 of 2441
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643
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Statistical test on two phylogenetically remote groups
phylogeny ANOVA
2.7 years ago by liorglic ★ 1.5k
3
votes
3
replies
1.5k
views
samtools markdup in Rsamtools
samtools R Rsamtools
updated 2.3 years ago by 45k • written 2.7 years ago by • 0
0
votes
0
replies
647
views
Sequence Homology locator
Sequence Homology Genome finder
2.7 years ago by himalayan_yeti • 0
3
votes
4
replies
1.6k
views
How to find the most frequent alternative-splicing event from DEXSEQ data?
DESEQ RNA-SEQ DEXSEQ
2.7 years ago by STARDUST ▴ 10
6
votes
3
replies
1.4k
views
To batch correct or analyse separately?
scRNA-seq batch-effect
updated 15 months ago by 45k • written 2.7 years ago by ▴ 170
1
vote
2
replies
1.5k
views
Issue with hmmcalibrate during tutorial.
hmmsearch hmmbuild hmmer hmmcalibrate
2.7 years ago by apcreyes29 • 0
1
vote
4
replies
1.5k
views
SNP calling
SNP GATK
updated 2.7 years ago by ★ 3.1k • written 2.7 years ago by ▴ 10
0
votes
0
replies
921
views
News: Course - INTRODUCTION TO PYTHON PROGRAMMING FOR BIOLOGISTS
Programming Python
updated 2.7 years ago by 45k • written 2.7 years ago by ★ 2.7k
5
votes
2
replies
1.4k
views
How to merge unique/non overlapping genes between 2 gene model GFF3 files?
gff3
updated 2.7 years ago by 9.3k • written 2.7 years ago by ★ 5.4k
0
votes
0
replies
581
views
gistic- overlapp
CNV GISTIC TCGA
2.7 years ago by Hanie • 0
0
votes
0
replies
681
views
Protocol to detect chromosomal ploidy from WGS VCF?
wgs ploidy
2.7 years ago by optimistsso4co3 ▴ 140
0
votes
0
replies
532
views
SpliceAi same variant , different score
SpliceAi
updated 2.7 years ago by 166k • written 2.7 years ago by • 0
0
votes
0
replies
654
views
Unrooted consensus tree [Bio.Phylo]
consensus phylo biopython
2.7 years ago by Jimpix ▴ 10
0
votes
6
replies
4.2k
views
PLINK2 selecting variants based on INFO score
plink2
2.7 years ago by m.c.roozen • 0
0
votes
3
replies
1.6k
views
DESeq2 results function runs very slow on Windows 10
r deseq2
updated 2.7 years ago by 22k • written 2.7 years ago by • 0
3
votes
2
replies
1.1k
views
How can I convert this pairwise format to fasta?
fasta python bash
updated 2.7 years ago by 154k • written 2.7 years ago by ▴ 170
0
votes
3
replies
2.0k
views
Trimmomatic
Trimmomatic RNA quality-check
2.7 years ago by Monia • 0
1
vote
0
replies
677
views
What is the difference between gseapy.prerank and gseapy.gsea?
gseapy gsea
2.7 years ago by bioinfo ▴ 160
1
vote
2
replies
855
views
When you convert a BAM back into a FastQ do you get the original Fastq?
bam FastQ
updated 2.7 years ago by 154k • written 2.7 years ago by • 0
3
votes
6
replies
1.9k
views
Which file and data structure is used to create volcano plot from scRNA-Seq experiment?
plot Volcano
2.7 years ago by Chris ▴ 360
1
vote
1
reply
908
views
bwa mem duration?
performance mapping bwa
updated 2.7 years ago by 89k • written 2.7 years ago by ▴ 120
10
votes
9
replies
33k
views
8 follow
Translating gene names to entrez id's
database annotation biopython gene python
updated 22 months ago by 45k • written 4.6 years ago by ▴ 10
2
votes
4
replies
1.9k
views
Gene ontology with locus tags
ontology locus gene tags
updated 2.7 years ago by ★ 3.1k • written 2.7 years ago by ▴ 10
3
votes
5
replies
1.7k
views
High downstream gene expression
downstream High Gene expression
updated 2.7 years ago by 22k • written 2.7 years ago by ▴ 10
2
votes
9
replies
3.5k
views
Clustering and dynamic tree cutting
dynamicTreeCut Clustering data RNAseq cutreeDynamic
updated 15 months ago by 3.9k • written 2.7 years ago by ▴ 10
0
votes
6
replies
1.9k
views
STAR is running but .sam file size does not increase after hours mapping
STAR RNA-seq mapping SAM
updated 2.7 years ago by 154k • written 2.7 years ago by ▴ 50
3
votes
4
replies
2.0k
views
Annotating ENS codes to gene name
expression RNA-seq DEseq2
updated 2.7 years ago by ▴ 320 • written 2.7 years ago by ▴ 60
0
votes
5
replies
2.4k
views
HTSeq error processing GFF file
HTSeq GFF GTF
updated 2.7 years ago by ★ 2.5k • written 2.7 years ago by ▴ 190
0
votes
0
replies
665
views
which tool to use for Transposon structure finding CENSOR or repeat masker ??
transposon DNA repeat CENSOR masker
2.7 years ago by manaswiniparija3 ▴ 60
4
votes
3
replies
1.3k
views
Using Entrez Utilities to query the Nucleotide database by collection_date
ncbi entrez
updated 2.6 years ago by ▴ 10 • written 2.7 years ago by ▴ 30
0
votes
0
replies
543
views
scATAC merging of files
Signac scATAC-seq
2.7 years ago by bioinformatics.girl ▴ 30
0
votes
2
replies
1.9k
views
Manual Polygenic Risk Score calculation
calculation steps PRS
updated 16 months ago by ▴ 50 • written 2.7 years ago by ▴ 20
7
votes
9
replies
6.6k
views
2D structure of a custom protein (not in any databases) from a PDB file.
PDB protein-structure Pymol
updated 15 months ago by ★ 2.1k • written 2.7 years ago by ▴ 80
0
votes
0
replies
595
views
what does ALT ID DUP refer to when ALT ID for copy number are already specified
ALT ID CNV VCF
2.7 years ago by anubratadas ▴ 20
0
votes
0
replies
570
views
VNTR genotyping
NGS VNTR genotyping
2.7 years ago by Genotepes ▴ 950
0
votes
0
replies
698
views
Which AF column do I use from TCGA data in maftools
vcf2maf sequencing genome WES maf
2.7 years ago by CH1374 ▴ 10
0
votes
3
replies
1.7k
views
Faking hh-suite workflow / alignment output
alignment hhsuite
updated 2.7 years ago by ★ 30k • written 2.7 years ago by ▴ 40
0
votes
5
replies
1.6k
views
RNASeq differential expression masked by pathways disregulation
normalization batch RNA-seq
updated 15 months ago by 45k • written 2.7 years ago by ▴ 130
0
votes
0
replies
588
views
Chloroplast genome phylogenetic analysis
Inverted region Chloroplast genome Phylogenetic analysis SSC
2.7 years ago by a.bibek52 ▴ 10
1
vote
0
replies
684
views
mVISTA annotation
alignment Annotation S-LAGAN mVISTA
2.7 years ago by a.bibek52 ▴ 10
0
votes
1
reply
1.1k
views
Create a new seurat object using one cluster identified in a previous seurat object
object seurat Create clusterization
updated 2.7 years ago by ▴ 80 • written 2.7 years ago by • 0
4
votes
2
replies
927
views
Analyzing bulk RNA-seq
RNAseq
updated 2.7 years ago by 15k • written 2.7 years ago by • 0
0
votes
5
replies
1.6k
views
Why am I getting only one common value when comparing two excel files?
python pandas excel
updated 2.7 years ago by 11k • written 2.7 years ago by • 0
2
votes
4
replies
1.7k
views
Alien-hunter outputs
alien-hunter
2.7 years ago by schlogl ▴ 180
1
vote
13
replies
2.5k
views
RNAseq for DE purpose
RNAseq
updated 2.7 years ago by 15k • written 2.7 years ago by • 0
0
votes
0
replies
493
views
Identifying off-target mutation frequency in Bacterial genomes
dCas9-deaminase off-target SNPS WGS dCas9
2.7 years ago by pd378 • 0
5
votes
5
replies
1.5k
views
Simulating metatranscriptomic shotgun reads
metatranscriptomic RNA simulated-reads shotgun-sequencing
updated 2.7 years ago by ★ 30k • written 2.7 years ago by ▴ 100
0
votes
0
replies
671
views
News: Eukaryotic Metabarcoding course
eDNA Metabarcoding
updated 2.7 years ago by 45k • written 2.7 years ago by ★ 2.7k
1
vote
2
replies
927
views
DESeq2 code to perform DEG analysis
DESeq2 DEG
updated 2.6 years ago by 45k • written 2.7 years ago by • 0
0
votes
0
replies
596
views
SVA correction reduces ability to detect genes as differential expressed?
gene-expression SVA RNA-seq batch-effect
updated 15 months ago by 45k • written 2.7 years ago by ▴ 60
122,020 results • Page 304 of 2441
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Comment: combine VCF from diploid reference/haplotypes for the same sample
Answer: HIV NL4-3 transcriptome fasta
ORFanage: by-reference protein annotation and comparison for transcriptome assembly
Mugsy Error: Can't find delta file....
A: Mugsy Error: Can't find delta file....
Answer: Variant Normalization
SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
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Recent Replies
Comment: HDOCK Server Error! by GenoMax 154k
This could be caused by the line endings that differ between macOS and Windows. Generally a utility like `dos2unix` can help fix this. You …
Comment: What is the length of the longest ORF appearing in reading frame 2 of any of the by Mensur Dlakic ★ 30k
Generally speaking, we are not here to provide code review service and/or fix code for what appears to be a school assignment. If you have …
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Istvan Albert 103k
We don't have 6 minutes to watch something without even knowing what it does. I would recommend that you provide a brief explanation of wh…
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Yang • 0
Thanks for the reply, I simply recorded the screen and used brave to integrate fastqc analysis. You can click the link below to view. In ge…
Answer: Variant Normalization by Istvan Albert 103k
The purpose of normalization is to ensure that identical variants are represented identically. When not normalized, the same variants may …
Answer: Should differential expression analysis be incorporated in cross validation for by i.sudbery 22k
Yes, their would potentially be data leakage if you perform the DE before dividing your datasets into folds. Its unclear how much of a prob…
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Istvan Albert 103k
I visited the website, but I couldn't understand what problem the software solves. You need to do a much better job of communicating the p…
Comment: Choosing enrichment analysis tool by i.sudbery 22k
How have these gene lists been obtained?
Comment: NOVOPlasty assembly fails with “INVALID SEED” using first read as seed by GenoMax 154k
> I used the first read sequence from ERR322446.filtered.A.fq as the seed `ERR322446` appears to be a human sample. Did you convert the …
Answer: Issue with Snippy 4.6.0 by GenoMax 154k
> Each individual Snippy run completes successfully and reports multiple variants When you run `snippy-core` there is no reference provid…
Comment: Quantification using salmon in alignment-based mode after minimap2 run by Assa Yeroslaviz ★ 1.9k
Hi Rob, sorry for the late question. I was wondering though, if I can also quantify transposable elements using oarfish? Should I increas…
Answer: 1 vs 1 DEG analysis in scrna seq data by ATpoint 89k
The only option you have is to treat every single cell as a replicate. That has the obvious downside that any effect can be a donor-unique …
Answer: GUI commercial software for 10x single cell gene expression analysis by firestar ★ 1.7k
An open-source option: [kana](https://www.kanaverse.org/kana/).
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Edward • 0
Yes, we plan to make English the primary language of the Brave UI.
Comment: Reasonable number of SNPs in a bacterial genome. by michael.ante ★ 4.0k
If your bacterial species is a (human) pathogen, you might want to check outbreak analysis papers of that species. In general, you find t…
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