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116,664 results • Page
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7
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Post-imputation plot
michigan-imputation-server
quality-control
updated 15 minutes ago by
Ram
43k • written 22 minutes ago by
kl
▴ 10
0
votes
3
replies
138
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 51 minutes ago by
noodle
▴ 570 • written 12 hours ago by
WUSCHEL
▴ 750
0
votes
3
replies
89
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated just now by
Wayne
★ 2.0k • written 3 hours ago by
Mariana
▴ 10
0
votes
1
reply
43
views
metagenomic virome quality assessment
viromics
metagenomics
updated 20 minutes ago by
Ram
43k • written 4 hours ago by
Petchimuthu
• 0
795
votes
167
replies
142k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
6
replies
53
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
updated 1 minute ago by
GenoMax
141k • written 1 hour ago by
salias
• 0
0
votes
0
replies
13
views
Using limma in methylation EM-seq?
EM-seq
methylation
1 hour ago by
Lluís R.
★ 1.2k
4
votes
7
replies
441
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
1 hour ago by
e.r.zakiev
▴ 200
0
votes
0
replies
19
views
Synteny analysis
bacterial
synteny
genome
updated 1 hour ago by
GenoMax
141k • written 1 hour ago by
Namil
• 0
0
votes
2
replies
40
views
Genbank File Format
gbkformat
updated 1 hour ago by
Mensur Dlakic
★ 27k • written 2 hours ago by
alenew.am
• 0
0
votes
5
replies
231
views
How should I make kallisto indexes?
kallisto
updated 10 minutes ago by
dsull
★ 5.9k • written 14 days ago by
bioinfo
▴ 150
0
votes
0
replies
36
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
2 hours ago by
SSSJec
• 0
0
votes
2
replies
53
views
Software to separate reads from different individuals
software
development
nanopore
1 hour ago by
njornet
▴ 20
0
votes
0
replies
23
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
3 hours ago by
David
• 0
3
votes
5
replies
154
views
High Malat-1 expression in single cell data
cell
analysis
single
updated 3 hours ago by
dsull
★ 5.9k • written 6 hours ago by
Kazo
▴ 10
0
votes
2
replies
74
views
How to update R on ubuntu
installation
update
R
apt-get
2 hours ago by
Bosberg
▴ 50
3
votes
0
replies
50
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
4 hours ago by
Biostar
2.7k
0
votes
1
reply
76
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 5 hours ago by
GenoMax
141k • written 9 hours ago by
Ruqaiya
• 0
0
votes
1
reply
228
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 5 hours ago by
trausch
★ 1.9k • written 16 days ago by
zec018
• 0
0
votes
0
replies
47
views
LEfSe
LEfSe
5 hours ago by
benkosta
• 0
0
votes
0
replies
38
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
3 hours ago by
Sara
▴ 30
1
vote
4
replies
302
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
3 hours ago by
hagl
▴ 10
0
votes
1
reply
79
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 6 hours ago by
Mohamed Abderrahmane
▴ 20 • written 7 hours ago by
matteo.levorato
• 0
0
votes
2
replies
88
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
6 hours ago by
Lluís R.
★ 1.2k
0
votes
1
reply
86
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 8 hours ago by
i.sudbery
19k • written 9 hours ago by
DOBI
• 0
0
votes
0
replies
53
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
10 hours ago by
atharvakarkare14
▴ 10
5
votes
16
replies
546
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
10 hours ago by
Ruqaiya
• 0
0
votes
1
reply
85
views
What should I consider as FASTA for dataset?
PDB
FASTA
updated 5 hours ago by
GenoMax
141k • written 10 hours ago by
Nafi
• 0
34
votes
21
replies
1.5k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 5 hours ago by
i.sudbery
19k • written 1 day ago by
noodle
▴ 570
0
votes
0
replies
46
views
Differential accessibility using DiffBinf
diffbind
11 hours ago by
Shloka
• 0
0
votes
0
replies
51
views
vg call vs vg surject
vg
variation
graphs
updated 5 hours ago by
GenoMax
141k • written 12 hours ago by
aliraza3119
• 0
0
votes
1
reply
77
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 5 hours ago by
GenoMax
141k • written 12 hours ago by
Winter
• 0
2
votes
7
replies
1.2k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 16 hours ago by
Gordon Smyth
★ 7.0k • written 8 months ago by
Calum
▴ 10
0
votes
1
reply
158
views
Finding batch and outlayers
Pca
updated 8 hours ago by
christopher medway
▴ 450 • written 17 hours ago by
Tigran
• 0
2
votes
2
replies
147
views
PDB related issue
rcsb
pdb
updated 17 hours ago by
noodle
▴ 570 • written 20 hours ago by
Nafi
• 0
0
votes
0
replies
77
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
8 hours ago by
carlopecoraro2
★ 2.5k
0
votes
7
replies
286
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 3 hours ago by
dsull
★ 5.9k • written 22 hours 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 11 hours ago by
Ram
43k • written 8 months ago by
Gio
• 0
2
votes
5
replies
401
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
22 hours ago by
ashaneev07
▴ 20
0
votes
1
reply
124
views
Downloading full alignments from Pfam
pfam
updated 1 day ago by
GenoMax
141k • written 1 day ago by
bef1
• 0
0
votes
1
reply
715
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 1 day ago by
Francesco
▴ 10 • written 3.3 years ago by
gt
▴ 30
2
votes
2
replies
245
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 8 hours ago by
i.sudbery
19k • written 3 days ago by
vanbelj
▴ 40
0
votes
0
replies
88
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 1 hour ago by
dariober
14k • written 1 day ago by
rene.j.erhardt
▴ 20
1
vote
3
replies
243
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 23 hours ago by
ATpoint
82k • written 1 day ago by
Francesco
▴ 10
0
votes
0
replies
113
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
1 day ago by
tnminh89
▴ 10
0
votes
0
replies
134
views
Extract protein sequence
fasta
alighment
blast
1 day ago by
anna
▴ 20
0
votes
0
replies
119
views
Filter low express genes in microarray data
microarray
1 day ago by
Chris
▴ 260
0
votes
1
reply
304
views
absolute path for symbolic links in Snakefile
Snakemake
updated 1 day ago by
Jesse
▴ 740 • written 9 days ago by
yifangt86
▴ 60
0
votes
2
replies
317
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 1 day ago by
Jesse
▴ 740 • written 4 days ago by
Broccoli
• 0
2
votes
3
replies
311
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 1 day ago by
Arup Ghosh
3.2k • written 2 days ago by
chaco001
▴ 40
116,664 results • Page
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Answer: what is the purpose of indexing the reference genome (Kallisto)
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Recent Replies
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
by
salias
• 0
Following your advice, I checked the primer and adapters sequences and edited the question accordingly
Comment: How should I make kallisto indexes?
by
dsull
★ 5.9k
We can't phase them out per se, because ``kallisto index`` is still the engine responsible for creating the index under the hood (and there…
Comment: When to use .vcf or .gvcf files from GATK HaplotypeCaller?
by
Medhat
9.7k
"./." in your gVCF files typically indicates a lack of information or uncertainty about the genotype at that particular position. This co…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
by
salias
• 0
Fungal ITS2 region (length is really variable so read-through can be an issue)
Answer: Is it possible to bulk download files from GEO repository?
by
noodle
▴ 570
Also try the NCBI AWS bucket transfer tool. It's extremely convenient, however it's not instantaneous and you need to have a (paid) AWS acc…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
by
GenoMax
141k
Check a random sampling of reads to make sure the adapters are being removed. You may also want to blast a few reads to ensure that there i…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
by
salias
• 0
Many thanks for your comment. If read-through is happening, shouldn't Cutadapt being taking care of that there? I provided to the Cutadapt …
Comment: How should I make kallisto indexes?
by
bioinfo
▴ 150
Thank you. I will read the documentation you attached. Are you going to slowly phase out the not kb ref commands? Also, does the t2g.txt fi…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
by
GenoMax
141k
> I need to understand why is this happening More than likely you have library fragments that are shorter than the length of sequencing. W…
Comment: Genbank File Format
by
Mensur Dlakic
★ 27k
I think this is a question for CLC support. It should be trivial for them to combine these fields into one. In other words, you need a bett…
Answer: Programmatically retrieving positions of protein active site residues
by
Mensur Dlakic
★ 27k
Although this probably doesn't qualify as `programmatically retrieving positions`, you can always do it by sequence alignments. This can be…
Answer: metagenomic virome quality assessment
by
Mensur Dlakic
★ 27k
The error message points to a problem with `prodigal-gv`. What happens when you type `prodigal-gv` on the command line? It is never a go…
Comment: Programmatically retrieving positions of protein active site residues
by
Wayne
★ 2.0k
"I have seen other similar posts but a lot of the tools and websites suggested are down." Please show & share your research as part of you…
Comment: Software to separate reads from different individuals
by
njornet
▴ 20
No... the extracted sample is already a mix so no way to barcode
Comment: Very low RNA splicing rate for pulmonary AT2 cells
by
e.r.zakiev
▴ 200
For anyone it might be useful: a colleague of mine, who was not dumb to use the wrong annotation `gtf` as I did, also observed an important…
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