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116,714 results • Page
2 of 2335
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0
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271
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News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
2 days ago by
David Langenberger
11k
0
votes
0
replies
122
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
2 days ago by
8armed
• 0
0
votes
1
reply
173
views
Deseq2
Deseq2
updated 2 days ago by
Jack Tierney
▴ 360 • written 2 days ago by
Sudip
• 0
1
vote
1
reply
204
views
Polishing genome assembly
polishing
Nanopore
PacBio
updated 2 days ago by
Michael
54k • written 2 days ago by
Lissa Cruz Saavedra
• 0
5
votes
3
replies
248
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 2 days ago by
Lluís R.
★ 1.2k • written 2 days ago by
이민경[학생](대학원 융합의과학과)
• 0
2
votes
2
replies
179
views
MA plot of shrunken fold change
MA-plot
Deseq2
updated 2 days ago by
ATpoint
82k • written 2 days ago by
Sudip
• 0
1
vote
2
replies
209
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 1 day ago by
Ram
43k • written 2 days ago by
Ravita
• 0
0
votes
0
replies
104
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
2 days ago by
Adyasha
• 0
0
votes
0
replies
107
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
2 days ago by
fanglujing
▴ 60
0
votes
0
replies
122
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
2 days ago by
Jacob
• 0
0
votes
3
replies
725
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 2 days ago by
weidonglu
• 0 • written 21 months ago by
JZX
• 0
0
votes
4
replies
242
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq
GO
updated 2 days ago by
Ram
43k • written 2 days ago by
Hamtaro
▴ 50
0
votes
1
reply
172
views
Differential Accessibility
DiffBind
updated 2 days ago by
Ram
43k • written 2 days ago by
Shloka
• 0
0
votes
3
replies
263
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 2 days ago by
GenoMax
142k • written 2 days ago by
kim
• 0
3
votes
2
replies
353
views
Extract protein sequence
fasta
alignment
blast
1 day ago by
anna
▴ 20
3
votes
3
replies
303
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 2 days ago by
noodle
▴ 580 • written 3 days ago by
WUSCHEL
▴ 750
0
votes
1
reply
155
views
metagenomic virome quality assessment
viromics
metagenomics
updated 2 days ago by
Ram
43k • written 3 days ago by
Petchimuthu
• 0
3
votes
7
replies
303
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
2 days ago by
salias
• 0
0
votes
0
replies
117
views
Using limma in methylation EM-seq?
EM-seq
methylation
2 days ago by
Lluís R.
★ 1.2k
4
votes
7
replies
564
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
2 days ago by
e.r.zakiev
▴ 200
0
votes
0
replies
119
views
Synteny analysis
bacterial
synteny
genome
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Namil
• 0
0
votes
4
replies
229
views
Genbank File Format
gbkformat
2 days ago by
alenew.am
• 0
0
votes
5
replies
390
views
How should I make kallisto indexes?
kallisto
updated 2 days ago by
dsull
★ 5.9k • written 16 days ago by
bioinfo
▴ 150
0
votes
0
replies
211
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
2 days ago by
SSSJec
• 0
0
votes
3
replies
200
views
Software to separate reads from different individuals
software
development
nanopore
updated 2 days ago by
GenoMax
142k • written 2 days ago by
njornet
▴ 20
0
votes
0
replies
89
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
3 days ago by
David
• 0
4
votes
5
replies
274
views
High Malat-1 expression in single cell data
cell
analysis
single
updated 3 days ago by
dsull
★ 5.9k • written 3 days ago by
Kazo
▴ 10
0
votes
2
replies
181
views
How to update R on ubuntu
installation
update
R
apt-get
2 days ago by
Bosberg
▴ 50
4
votes
0
replies
123
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
3 days ago by
Biostar
2.7k
0
votes
1
reply
127
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Ruqaiya
• 0
0
votes
1
reply
270
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 3 days ago by
trausch
★ 1.9k • written 19 days ago by
zec018
• 0
0
votes
0
replies
98
views
LEfSe
LEfSe
3 days ago by
benkosta
• 0
0
votes
0
replies
83
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
3 days ago by
Sara
▴ 30
1
vote
4
replies
375
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
3 days ago by
hagl
▴ 10
0
votes
3
replies
190
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 2 hours ago by
Mohamed Abderrahmane
▴ 20 • written 3 days ago by
matteo.levorato
• 0
0
votes
2
replies
147
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
3 days ago by
Lluís R.
★ 1.2k
0
votes
1
reply
136
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 3 days ago by
i.sudbery
19k • written 3 days ago by
DOBI
• 0
0
votes
0
replies
96
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
3 days ago by
atharvakarkare14
▴ 20
5
votes
16
replies
669
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
3 days ago by
Ruqaiya
• 0
0
votes
2
replies
190
views
What should I consider as FASTA for dataset?
PDB
FASTA
2 days ago by
Nafi
• 0
38
votes
24
replies
1.8k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 2 days ago by
i.sudbery
19k • written 4 days ago by
noodle
▴ 580
0
votes
0
replies
86
views
Differential accessibility using DiffBinf
diffbind
3 days ago by
Shloka
• 0
0
votes
0
replies
92
views
vg call vs vg surject
vg
variation
graphs
updated 3 days ago by
GenoMax
142k • written 3 days ago by
aliraza3119
• 0
0
votes
1
reply
126
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Winter
• 0
2
votes
7
replies
1.3k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 3 days ago by
Gordon Smyth
★ 7.1k • written 8 months ago by
Calum
▴ 10
0
votes
1
reply
199
views
Finding batch and outlayers
Pca
updated 3 days ago by
christopher medway
▴ 450 • written 3 days ago by
Tigran
• 0
2
votes
2
replies
193
views
PDB related issue
rcsb
pdb
updated 3 days ago by
noodle
▴ 580 • written 3 days ago by
Nafi
• 0
0
votes
0
replies
107
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
3 days ago by
carlopecoraro2
★ 2.5k
0
votes
8
replies
410
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 1 day ago by
LauferVA
4.2k • written 3 days ago by
jinyu
▴ 10
0
votes
9
replies
2.5k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 3 days ago by
Ram
43k • written 8 months ago by
Gio
• 0
116,714 results • Page
2 of 2335
Recent Votes
Comment: Problem with data downloaded from Short Reads Archive (SRA)
Comment: Problem with data downloaded from Short Reads Archive (SRA)
Comment: Problem with data downloaded from Short Reads Archive (SRA)
Comment: Problem with data downloaded from Short Reads Archive (SRA)
A: What is the difference between GRCh37 and hs37? And hg19?
A: Decoy In Reference Assembly
A: Decoy In Reference Assembly
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eesiribloom
▴ 80
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g.persic1991
• 0
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massa.kassa.sc3na
▴ 600
Teacher
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Recent Replies
Answer: Downsampling long-read BAM files
by
eesiribloom
▴ 80
random downsampling of bam files is now possible using [rasusa][1] [v1.0.0][2] with the `aln` subcommand [1]: https://github.com/mbh…
Comment: Problem with data downloaded from Short Reads Archive (SRA)
by
GenoMax
142k
Use `vdb-validate` included in `sratoolkit` to check your `*.sra` files for integrity.
Comment: Problem with data downloaded from Short Reads Archive (SRA)
by
ATpoint
82k
This `fastq-dump --split-files *.sra` gives you fastq files. I am not sure how, with the given information, one might debug your problem. A…
Answer: What analysis suitable to identify similarly expressed genes between two samples
by
ATpoint
82k
DESeq2 has a "lessAbs" test which gioves you a pvalue that tests whether a fold change is **below** a user-defined threshold, see https://b…
Comment: RNAseq one control two conditions, shared and exclusive genes
by
Mohamed Abderrahmane
▴ 20
In your table RawCounts, keep only the columns corresponding to condition 1 and the control. Edit the table sampleTable to align with your …
Comment: Problem with data downloaded from Short Reads Archive (SRA)
by
Begonia_pavonina
▴ 150
Thank you @atpoint, I did already investigate this error on the DADA2 github. It seems that the "BiocParallel" error can be due to multipl…
Comment: Discrepancy in read counts from fastq
by
GenoMax
142k
Try `reformat.sh` from BBMap suite and its sampling parameters. You may get a third answer. Programs do some approximations so it is probab…
Comment: Problem with data downloaded from Short Reads Archive (SRA)
by
ATpoint
82k
One cannot help you with this. The error is from R, yet you show not a single line of R code.
Comment: Bacterial plasmid analysis
by
Daria
▴ 10
I am the colleague! My tool groups together plasmids based on two genetic distances: containment (how much of the smaller plasmid's sequenc…
Comment: Subsetting and merging back Seurat Object brings different results
by
Bine
▴ 60
Ok I think I know what happened. The order of cells changed, otherwise its the same: ![image](https://github.com/satijalab/seurat/assets/7…
Answer: Bacterial plasmid analysis
by
shenwei356
8.5k
My colleague has an unpublished tool for plasmid analysis (clustering), and it has really good results. You might have a try. https://githu…
Comment: Odd alignment question/finding
by
ATpoint
82k
bwa mem is not fully deterministic, see from the developer: https://www.biostars.org/p/238628/#238817
Comment: How to perform single cell multimodal integration using Seurat for Geo datasets
by
ATpoint
82k
It's funny that you ask because the paper that these data were used for is called `Integrated analysis of multimodal single-cell data` from…
Comment: Odd alignment question/finding
by
liorglic
★ 1.4k
I can't come up with an explanation, but two things you can try for debugging are: 1) look at the fastp stats - do they add up and make sen…
Answer: Bacterial plasmid analysis
by
Mensur Dlakic
★ 27k
If you put all your sequences in separate files but in the same directory, this program will build a cladogram based on average nucleotide …
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