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122,011 results • Page 286 of 2441
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12
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8
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3.8k
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Sorting a STAR-output bam file with samtools leads to a significant reduction in size of the sorted bam file
samtools STAR
2.6 years ago by e.r.zakiev ▴ 260
0
votes
1
reply
932
views
Chiseq files for deseq2
countMatrix deseq2 Chipseq
updated 2.6 years ago by 4.7k • written 2.6 years ago by • 0
1
vote
2
replies
1.3k
views
RNA-seq data analysis (prokaryotes) featurecounts with
featureCounts RNA-Seq
2.6 years ago by Pegasus ▴ 130
1
vote
1
reply
1.1k
views
News: Sign-ups for the St. Jude KIDS23 BioHackathon (May 3-5th) open through March 15th!
stjude hackathon
2.6 years ago by jared.andrews07 ★ 19k
1
vote
3
replies
1.1k
views
ENA Submitted Files Download
ENA
updated 2.6 years ago by 4.7k • written 2.6 years ago by • 0
0
votes
0
replies
862
views
Problem with homer in findMotifs.pl when using input and bg fasta
motif Homer findMotifs.pl
updated 2.6 years ago by 154k • written 2.6 years ago by • 0
1
vote
3
replies
1.2k
views
Find genes which are related to SNPs
NCBI SNP
updated 2.6 years ago by 154k • written 2.6 years ago by • 0
2
votes
1
reply
1.5k
views
Transcript variants conversion from Ensembl ENST to NM
Ensembl transcript RefSeq
updated 2.6 years ago by ★ 2.4k • written 2.6 years ago by • 0
2
votes
2
replies
1.4k
views
ORFik: error making Txdb from GTF and fasta files
gff3 gtf ORFik
2.4 years ago by Estefania ▴ 30
0
votes
3
replies
2.4k
views
Get Exon Sequence from biomaRt given ENST transcript ID and exon number.
ensembl R biomart
2.6 years ago by acererak ▴ 10
0
votes
3
replies
1.9k
views
Alt allele - after bcftools norm
bcftools GATK VCF
updated 2.6 years ago by 6.2k • written 2.6 years ago by ▴ 100
7
votes
1
reply
1.9k
views
How to use filterbyExpr with DESeq2?
DESeq2 RNA-seq edgeR
updated 2.6 years ago by 45k • written 2.6 years ago by ▴ 110
0
votes
0
replies
638
views
Diamond blast functional annotation
blast Diamond
updated 2.6 years ago by 45k • written 2.6 years ago by • 0
3
votes
1
reply
913
views
Snakemake error to build synteny from BUSCO .tsv
synteny BUSO
updated 2.6 years ago by ▴ 540 • written 2.6 years ago by ▴ 110
1
vote
2
replies
2.1k
views
How to create PSSM files?
PSI-BLAST PSSM
2.6 years ago by Manzoor • 0
0
votes
0
replies
948
views
Stage 8 error on Desmond
Maestro Molecular-Simulation Desmond Schrodinger
updated 2.6 years ago by 45k • written 2.6 years ago by • 0
0
votes
0
replies
1.6k
views
Job: Bioinformatics Officer - South Australian Genomics Centre (SAGC), Australia
genomics masters Australia postdoc
updated 2.6 years ago by 45k • written 2.6 years ago by ▴ 50
0
votes
0
replies
1.5k
views
Job: Bioinformaticican/Computational Biologist - South Australian Genomics Centre (SAGC), Australia
genomics Australia postdoc
updated 2.6 years ago by 45k • written 2.6 years ago by ▴ 50
4
votes
4
replies
2.4k
views
Why my single cell cluster is splitted?
clustering single-cell
updated 2.6 years ago by ★ 30k • written 2.6 years ago by ▴ 110
0
votes
1
reply
1.9k
views
Parser EggNOG-mapper annotation output using pythom
EggNOG-mapper Python
updated 2.6 years ago by ★ 30k • written 2.6 years ago by ▴ 20
4
votes
1
reply
1.8k
views
How to create a graph that shows pairwise Fst values at single SNP loci across the all chromosomes in R
R Fst graph
updated 2.6 years ago by ★ 4.3k • written 2.6 years ago by ▴ 40
1
vote
2
replies
1.5k
views
Bioinformatics package
python
updated 2.6 years ago by 48k • written 2.6 years ago by ▴ 20
1
vote
4
replies
1.5k
views
correlation between protein expression and RNA read counts
RNAseq protein-expression correlation
updated 2.6 years ago by ★ 30k • written 2.6 years ago by ▴ 40
0
votes
0
replies
651
views
ATAC seq fragment file
ATAC-seq
updated 2.6 years ago by 45k • written 2.6 years ago by ▴ 360
0
votes
0
replies
532
views
differential expression analysis of tRFs
DGE RNA-seq tRF tRNA
updated 2.6 years ago by 45k • written 2.6 years ago by • 0
0
votes
0
replies
664
views
Double-pass with STAR for better detection of spliced variants in assessing quality of FFPE RNAseq data: should I go for it?
RNA-seq STAR
updated 2.6 years ago by 45k • written 2.6 years ago by ▴ 260
5
votes
6
replies
2.6k
views
I can not allocate ram memory for WSL2
WSL2
2.6 years ago by ailton • 0
0
votes
2
replies
843
views
how i can merge two file with more than one condition in R?
R
updated 2.6 years ago by 45k • written 2.6 years ago by • 0
5
votes
4
replies
2.3k
views
STARsolo issue
STARsolo scRNAseq
2.5 years ago by friguiahlem8 ▴ 30
3
votes
7
replies
3.0k
views
Inclusion of R script in shiny application
shiny script
2.6 years ago by mrashad ▴ 80
0
votes
2
replies
1.4k
views
SRA prefetch error
prefetch rnaseq
updated 2.6 years ago by ★ 3.1k • written 2.6 years ago by ▴ 10
2
votes
0
replies
1.1k
views
Herald: The Biostar Herald for Monday, March 13, 2023
herald
2.6 years ago by Biostar 3.6k
1
vote
0
replies
651
views
News: Course - BIOINFORMATIC ANALYSIS OF TRANSPOSABLE ELEMENTS
Transposable-Elements TE Genome-Assembly
updated 2.6 years ago by 45k • written 2.6 years ago by ★ 2.6k
0
votes
9
replies
1.8k
views
Tissue-dependent usage of exons
alternative splicing exons usage
2.6 years ago by mariannapauletto ▴ 90
2
votes
2
replies
994
views
Could I consider an ENCODE experiment with two library as two replicates for differential analysis?
ENCODE
2.6 years ago by zau saa ▴ 150
0
votes
0
replies
551
views
Does it make sense to add together the concentrations of different stereospecifically numbered lipids?
lipidomics masss spectrometry metabolomics lipids
2.6 years ago by Katia • 0
103
votes
27
replies
100k
views
21 follow
Extract Sub-Set Of Regions From Vcf File
vcf tabix genome filter
updated 2.4 years ago by • 0 • written 13.4 years ago by ▴ 850
0
votes
6
replies
3.0k
views
cellranger-arc mkfastq Error: bcl2fastq was killed with signal -11
bcl2fastq cellranger-arc mkfastq cellranger
updated 2.6 years ago by ▴ 30 • written 2.7 years ago by ▴ 60
1
vote
2
replies
1.9k
views
Cellranger pipeline 3.1.0 demultiplexing (cellranger demux)
scRNA python cellranger
2.6 years ago by Emily ▴ 70
0
votes
0
replies
556
views
Differentially methylated regions between genomes
wgbs methylation plant methyltome
2.6 years ago by Sebastian • 0
0
votes
0
replies
1.2k
views
Blog: WGS vs WES: Which Genetic Sequencing Method is Right for You?
WGS WES genome-sequencing
2.6 years ago by Novogene ▴ 510
0
votes
2
replies
1.5k
views
Extract sequences from the blast results
Sequences Extract
updated 2.6 years ago by 154k • written 2.6 years ago by ▴ 20
1
vote
1
reply
2.1k
views
Filtering VCF by specific tag in INFO field
bcftools vcf
updated 2.3 years ago by 45k • written 2.6 years ago by ▴ 30
0
votes
0
replies
622
views
Using RAST's API or as a command line tool‏‏
RAST command-line API
2.6 years ago by langziv ▴ 70
0
votes
1
reply
1.2k
views
Polishing PacBio or ONT with Illumina
pacbio polish ONT illumina
updated 2.6 years ago by • 0 • written 3.9 years ago by ▴ 440
3
votes
6
replies
1.6k
views
Chromosome "whole genome shotgun sequence" not found
samtools
updated 2.3 years ago by 45k • written 2.6 years ago by ▴ 40
0
votes
0
replies
829
views
Two factors plus time, LRT with DEseq2
deseq2 time-course
2.6 years ago by boczniak767 ▴ 880
0
votes
1
reply
907
views
Can't open Autodock and chembio3D
Autodock chembio3D
updated 2.5 years ago by • 0 • written 2.6 years ago by • 0
0
votes
0
replies
631
views
Calling with samtools mpileup calls fewer SNPs than expected.
variant-calling samtools mpileup
updated 2.3 years ago by 45k • written 2.6 years ago by ▴ 10
1
vote
4
replies
3.3k
views
normalize RNA seq pseudobulk after matrix creation
scRNA-seq pseudobulk r single-cell
updated 23 months ago by 45k • written 2.6 years ago by ▴ 50
122,011 results • Page 286 of 2441
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Comment: GUI commercial software for 10x single cell gene expression analysis
Comment: GUI commercial software for 10x single cell gene expression analysis
Comment: Pseudogene - scarce info
Comment: GUI commercial software for 10x single cell gene expression analysis
Manual Genome Curation using PretextView course
Answer: How to get proteins from GFF file resulted from MAKER annotation
Comment: DESeq2 on metagenome KO counts
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Recent Replies
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 …
Comment: DESeq2 on metagenome KO counts by ATpoint 89k
The DESeq2 developer has advised many times against DESeq2 for metagenomics. Please search for related posts over at support.bioconductor.o…
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