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48 results • Page
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34
votes
21
replies
1.5k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 4 hours ago by
i.sudbery
19k • written 1 day ago by
noodle
▴ 570
5
votes
16
replies
543
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
8 hours ago by
Ruqaiya
• 0
2
votes
11
replies
803
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 6 hours ago by
jkbonfield
★ 1.2k • written 12 days ago by
me
• 0
0
votes
9
replies
2.5k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 10 hours ago by
Ram
43k • written 8 months ago by
Gio
• 0
0
votes
7
replies
279
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 2 hours ago by
dsull
★ 5.9k • written 21 hours ago by
jinyu
▴ 10
4
votes
7
replies
434
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
30 minutes ago by
e.r.zakiev
▴ 200
2
votes
7
replies
1.2k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 15 hours ago by
Gordon Smyth
★ 7.0k • written 8 months ago by
Calum
▴ 10
1
vote
7
replies
338
views
Downsampling fastq file
downsample
fastq
updated 53 minutes ago by
Ram
43k • written 7 days ago by
marco.barr
▴ 80
1
vote
7
replies
428
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 1 hour ago by
bk11
★ 2.4k • written 4 days ago by
starswillfade
▴ 10
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma
gwas
updated 3 hours ago by
dimpleadiwal050896
• 0 • written 4.9 years ago by
ggman
▴ 90
2
votes
5
replies
399
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
21 hours ago by
ashaneev07
▴ 20
3
votes
5
replies
128
views
High Malat-1 expression in single cell data
cell
analysis
single
updated 2 hours ago by
dsull
★ 5.9k • written 5 hours ago by
Kazo
▴ 10
2
votes
5
replies
316
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
9 hours ago by
analyst
▴ 30
1
vote
4
replies
286
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
2 hours ago by
hagl
▴ 10
0
votes
3
replies
58
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated just now by
Mensur Dlakic
★ 27k • written 2 hours ago by
Mariana
▴ 10
1
vote
3
replies
336
views
PCA plot
DESeq2
PCAplot
updated 21 hours ago by
LauferVA
4.2k • written 4 days ago by
Aaliya
▴ 10
1
vote
3
replies
341
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 19 hours ago by
Mensur Dlakic
★ 27k • written 2 days ago by
O.rka
▴ 710
0
votes
3
replies
198
views
How should I make kallisto indexes?
kallisto
updated 56 minutes ago by
dsull
★ 5.9k • written 14 days ago by
bioinfo
▴ 150
0
votes
3
replies
280
views
CWl and toil singularity image e.g busybox? Thank you
toil
singularity
updated 51 minutes ago by
Ram
43k • written 4 months ago by
Fadi
• 0
1
vote
3
replies
240
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 22 hours ago by
ATpoint
82k • written 1 day ago by
Francesco
▴ 10
0
votes
2
replies
125
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 4 hours ago by
GenoMax
141k • written 10 hours ago by
WUSCHEL
▴ 750
2
votes
2
replies
242
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 7 hours ago by
i.sudbery
19k • written 3 days ago by
vanbelj
▴ 40
2
votes
2
replies
145
views
PDB related issue
rcsb
pdb
updated 16 hours ago by
noodle
▴ 570 • written 19 hours ago by
Nafi
• 0
0
votes
2
replies
38
views
Software to separate reads from different individuals
software
development
nanopore
30 minutes ago by
njornet
▴ 20
0
votes
2
replies
86
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
5 hours ago by
Lluís R.
★ 1.2k
0
votes
2
replies
58
views
How to update R on ubuntu
installation
update
R
apt-get
1 hour ago by
Bosberg
▴ 50
0
votes
1
reply
78
views
What should I consider as FASTA for dataset?
PDB
FASTA
updated 4 hours ago by
GenoMax
141k • written 9 hours ago by
Nafi
• 0
0
votes
1
reply
223
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 4 hours ago by
trausch
★ 1.9k • written 16 days ago by
zec018
• 0
0
votes
1
reply
85
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 7 hours ago by
i.sudbery
19k • written 8 hours ago by
DOBI
• 0
0
votes
1
reply
73
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 3 hours ago by
GenoMax
141k • written 11 hours ago by
Winter
• 0
0
votes
1
reply
72
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 4 hours ago by
GenoMax
141k • written 8 hours ago by
Ruqaiya
• 0
0
votes
1
reply
27
views
metagenomic virome quality assessment
viromics
metagenomics
and
updated 10 minutes ago by
Mensur Dlakic
★ 27k • written 2 hours ago by
Petchimuthu
• 0
0
votes
1
reply
156
views
Finding batch and outlayers
Pca
updated 7 hours ago by
christopher medway
▴ 450 • written 16 hours ago by
Tigran
• 0
0
votes
1
reply
21
views
Genbank File Format
gbkformat
updated 48 minutes ago by
GenoMax
141k • written 57 minutes ago by
alenew.am
• 0
0
votes
1
reply
75
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 5 hours ago by
Mohamed Abderrahmane
▴ 20 • written 6 hours ago by
matteo.levorato
• 0
0
votes
0
replies
44
views
LEfSe
LEfSe
4 hours ago by
benkosta
• 0
0
votes
0
replies
49
views
vg call vs vg surject
vg
variation
graphs
updated 4 hours ago by
GenoMax
141k • written 11 hours ago by
aliraza3119
• 0
0
votes
0
replies
75
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
6 hours ago by
carlopecoraro2
★ 2.5k
3
votes
0
replies
41
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
3 hours ago by
Biostar
2.7k
0
votes
0
replies
36
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
2 hours ago by
Sara
▴ 30
0
votes
0
replies
15
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
1 hour ago by
David
• 0
0
votes
0
replies
51
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
8 hours ago by
atharvakarkare14
▴ 10
0
votes
0
replies
25
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
1 hour ago by
SSSJec
• 0
0
votes
0
replies
6
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
illumina
cutadap
tile
paired-end
7 minutes ago by
salias
• 0
0
votes
0
replies
44
views
Differential accessibility using DiffBinf
diffbind
10 hours ago by
Shloka
• 0
0
votes
0
replies
14
views
Synteny analysis
bacterial
synteny
genome
updated 46 minutes ago by
GenoMax
141k • written 49 minutes ago by
Namil
• 0
0
votes
0
replies
87
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 20 minutes ago by
dariober
14k • written 1 day ago by
rene.j.erhardt
▴ 20
0
votes
0
replies
6
views
Using limma in methylation EM-seq?
EM-seq
methylation
20 minutes ago by
Lluís R.
★ 1.2k
48 results • Page
1 of 1
Recent Votes
Answer: Mapping ortholog human and mouse transcript
C: Kallisto missing Bootstrap
Answer: Very low RNA splicing rate for pulmonary AT2 cells
Answer: what is the purpose of indexing the reference genome (Kallisto)
The Biostar Herald for Monday, April 29, 2024
The Biostar Herald for Monday, April 29, 2024
Comment: NGS forensics: how to know if data is fabricated
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▴ 200
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★ 4.2k
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Recent Replies
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`, also observed an important issue of…
Answer: Very low RNA splicing rate for pulmonary AT2 cells
by
e.r.zakiev
▴ 200
Hello people sorry I am dumb the problem lied in the fact that I had mouse cells but my `.gtf` transcriptome file was for the human. Now wi…
Comment: Genbank File Format
by
GenoMax
141k
Can you indicate if you need to do this within CLC or can use an external solution (if someone provides it here). If you need to do this in…
Comment: Downsampling fastq file
by
Ram
43k
The file being PE should not matter. I'd recommend you open an issue on the seqtk github repo as this is starting to look like some sort of…
Comment: CWl and toil singularity image e.g busybox? Thank you
by
Ram
43k
Do the developers of toil mention biostars? Where do they direct their support requests to?
Comment: How should I make kallisto indexes?
by
dsull
★ 5.9k
As an additional note, all those ``--include-attribute`` stuff was basically to restrict the transcriptome to precisely the items that Cell…
Answer: How should I make kallisto indexes?
by
dsull
★ 5.9k
I recommend the ``kb ref`` method for two reasons: 1. The index created will yield more accurate mapping for datasets that have a substa…
Comment: Software to separate reads from different individuals
by
GenoMax
141k
Were these samples barcoded when they were run. If not then you won't be able to do much.
Comment: ScRNA data question
by
bk11
★ 2.4k
The approach you are using here is the old method. Seurat is updated to V5. Please try Seurat V5 integrative analysis described in the link…
Answer: How should I make kallisto indexes?
by
Bajaj
• 0
Hi, you can still use `kallisto index -i transcripts.index transcripts.fa` (extract the gz file) for making index files. I have tried it an…
Comment: How to update R on ubuntu
by
Bosberg
▴ 50
Thanks for the suggestion, but I get several lines of results (see below) and although there are directories called `"R"`, I can't find any…
Comment: High Malat-1 expression in single cell data
by
dsull
★ 5.9k
Malat1 is a lncRNA abundant in the nucleus. I guess if Malat1 is abundant and stable, makes sense it could be detect in high amounts in scR…
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