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51 results • Page
1 of 2
Sort: Rank
Rank
Views
Votes
Replies
0
votes
1
reply
172
views
Extract protein sequence
fasta
alignment
blast
updated 2 hours ago by
Ram
43k • written 1 day ago by
anna
▴ 20
0
votes
0
replies
25
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 2 hours ago by
Ram
43k • written 2 hours ago by
kl
▴ 10
0
votes
3
replies
164
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 3 hours ago by
noodle
▴ 570 • written 14 hours ago by
WUSCHEL
▴ 750
0
votes
4
replies
138
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 20 minutes ago by
Wayne
★ 2.0k • written 6 hours ago by
Mariana
▴ 10
0
votes
1
reply
63
views
metagenomic virome quality assessment
viromics
metagenomics
updated 2 hours ago by
Ram
43k • written 6 hours ago by
Petchimuthu
• 0
3
votes
7
replies
138
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
2 hours ago by
salias
• 0
0
votes
0
replies
30
views
Using limma in methylation EM-seq?
EM-seq
methylation
4 hours ago by
Lluís R.
★ 1.2k
4
votes
7
replies
467
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
3 hours ago by
e.r.zakiev
▴ 200
0
votes
0
replies
39
views
Synteny analysis
bacterial
synteny
genome
updated 4 hours ago by
GenoMax
141k • written 4 hours ago by
Namil
• 0
0
votes
2
replies
75
views
Genbank File Format
gbkformat
updated 3 hours ago by
Mensur Dlakic
★ 27k • written 4 hours ago by
alenew.am
• 0
0
votes
5
replies
269
views
How should I make kallisto indexes?
kallisto
updated 2 hours ago by
dsull
★ 5.9k • written 14 days ago by
bioinfo
▴ 150
0
votes
0
replies
59
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
5 hours ago by
SSSJec
• 0
0
votes
3
replies
100
views
Software to separate reads from different individuals
software
development
nanopore
updated 1 hour ago by
GenoMax
141k • written 5 hours ago by
njornet
▴ 20
0
votes
0
replies
35
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
5 hours ago by
David
• 0
3
votes
5
replies
168
views
High Malat-1 expression in single cell data
cell
analysis
single
updated 5 hours ago by
dsull
★ 5.9k • written 8 hours ago by
Kazo
▴ 10
0
votes
2
replies
88
views
How to update R on ubuntu
installation
update
R
apt-get
5 hours ago by
Bosberg
▴ 50
3
votes
0
replies
58
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
7 hours ago by
Biostar
2.7k
0
votes
1
reply
82
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 7 hours ago by
GenoMax
141k • written 12 hours ago by
Ruqaiya
• 0
0
votes
1
reply
233
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 8 hours ago by
trausch
★ 1.9k • written 17 days ago by
zec018
• 0
0
votes
0
replies
51
views
LEfSe
LEfSe
8 hours ago by
benkosta
• 0
0
votes
0
replies
41
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
6 hours ago by
Sara
▴ 30
1
vote
4
replies
314
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
6 hours ago by
hagl
▴ 10
0
votes
1
reply
83
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 9 hours ago by
Mohamed Abderrahmane
▴ 20 • written 9 hours ago by
matteo.levorato
• 0
0
votes
2
replies
93
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
9 hours ago by
Lluís R.
★ 1.2k
0
votes
1
reply
91
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 11 hours ago by
i.sudbery
19k • written 12 hours ago by
DOBI
• 0
0
votes
0
replies
57
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
12 hours ago by
atharvakarkare14
▴ 10
5
votes
16
replies
550
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
12 hours ago by
Ruqaiya
• 0
0
votes
1
reply
89
views
What should I consider as FASTA for dataset?
PDB
FASTA
updated 7 hours ago by
GenoMax
141k • written 12 hours ago by
Nafi
• 0
34
votes
22
replies
1.5k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
1 hour ago by
noodle
▴ 570
0
votes
0
replies
50
views
Differential accessibility using DiffBinf
diffbind
14 hours ago by
Shloka
• 0
0
votes
0
replies
54
views
vg call vs vg surject
vg
variation
graphs
updated 7 hours ago by
GenoMax
141k • written 15 hours ago by
aliraza3119
• 0
0
votes
1
reply
84
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 7 hours ago by
GenoMax
141k • written 15 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 19 hours ago by
Gordon Smyth
★ 7.1k • written 8 months ago by
Calum
▴ 10
0
votes
1
reply
164
views
Finding batch and outlayers
Pca
updated 10 hours ago by
christopher medway
▴ 450 • written 20 hours ago by
Tigran
• 0
2
votes
2
replies
151
views
PDB related issue
rcsb
pdb
updated 20 hours ago by
noodle
▴ 570 • written 23 hours ago by
Nafi
• 0
0
votes
0
replies
80
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
10 hours ago by
carlopecoraro2
★ 2.5k
0
votes
7
replies
297
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 6 hours ago by
dsull
★ 5.9k • written 1 day 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 14 hours ago by
Ram
43k • written 8 months ago by
Gio
• 0
2
votes
2
replies
249
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 11 hours ago by
i.sudbery
19k • written 3 days ago by
vanbelj
▴ 40
0
votes
0
replies
92
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 4 hours ago by
dariober
14k • written 1 day ago by
rene.j.erhardt
▴ 20
1
vote
3
replies
348
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology
metagenomics
database
enzymes
genomics
updated 23 hours ago by
Mensur Dlakic
★ 27k • written 2 days ago by
O.rka
▴ 710
4
votes
2
replies
232
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
2 hours ago by
pairedttest
▴ 10
1
vote
7
replies
443
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 5 hours ago by
bk11
★ 2.4k • written 4 days ago by
starswillfade
▴ 10
2
votes
5
replies
318
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
13 hours ago by
analyst
▴ 30
1
vote
7
replies
358
views
Downsampling fastq file
downsample
fastq
updated 4 hours ago by
Ram
43k • written 7 days ago by
marco.barr
▴ 80
2
votes
11
replies
807
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 10 hours ago by
jkbonfield
★ 1.2k • written 12 days ago by
me
• 0
0
votes
3
replies
308
views
CWl and toil singularity image e.g busybox? Thank you
toil
singularity
updated 4 hours ago by
Ram
43k • written 4 months ago by
Fadi
• 0
2
votes
4
replies
2.6k
views
When to use .vcf or .gvcf files from GATK HaplotypeCaller?
indel
gatk
calling
snp
variant
updated 3 hours ago by
Medhat
9.7k • written 23 months ago by
Vitor1
▴ 120
2
votes
5
replies
914
views
Retrieval of Active site information programmatically
Catalytic
Python
Active
PDB
site
Site
updated 2 hours ago by
Wayne
★ 2.0k • written 2.0 years ago by
arinjoy
• 0
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
2 hours ago by
anna
▴ 20
51 results • Page
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Recent Votes
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
Comment: How to calculate identity percentage between proteins contained in a FASTA file?
Comment: How to calculate identity percentage between proteins contained in a FASTA file?
Answer: How to use limma to find differentially expressed genes in response to a continu
Answer: How to use limma to find differentially expressed genes in response to a continu
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
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Recent Replies
Comment: Programmatically retrieving positions of protein active site residues
by
Wayne
★ 2.0k
Wow, I was shocked at this AI answer that looks to be a good start for using UniProt. Sharing it in case it is useful. (It will work in ses…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 570
> Can you clarify what you mean by "100% of reads pass cutadapt, even > though 70% of reads contain adapters and get trimmed. The header o…
Comment: Software to separate reads from different individuals
by
GenoMax
141k
If you have independent information available (e.g. genotype data for both individuals) then you *may* be able to assign reads based on the…
Answer: Extract protein sequence
by
Matthias Zepper
4.5k
You didn't mention what kind of organism you are working with and what kind of protein you are looking for? If it happens to be a microbia…
Comment: How to use limma to find differentially expressed genes in response to a continu
by
pairedttest
▴ 10
Thank you Gordon for your expertise. One question that I have now that I have a list of DE genes is how to interpret logFC of this continuo…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
by
salias
• 0
Yes I plan to use QIIME2, but I'm Cutadapting outside QIIME so its easier to MultiQC without importing/unzipping QZAs (and QIIME2 importing…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
by
GenoMax
141k
> 3' adapters were removed aprox. 90 times each one, so there sohuld not be read-through at all here Then you have data that has poor Q sc…
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…
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