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112,646 results • Page
1 of 2253
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Running Rockhopper from a command-line
command-line
rockhopper
java
just now by
langziv
▴ 50
0
votes
0
replies
1
view
bcftools error merging two VCFs: REF prefixes differ
bcftools
VCF
merge
just now by
Shane
• 0
0
votes
1
reply
162
views
Gene enrichment analysis of prokaryotes gene
prokaryotes
GO
enrichment
DEG
updated 8 minutes ago by
dthorbur
▴ 550 • written 4 days ago by
Genta
• 0
0
votes
1
reply
44
views
GWAS phenotype
R
GWAS
phenotype
updated 41 minutes ago by
dthorbur
▴ 550 • written 3 hours ago by
sooni
▴ 10
0
votes
0
replies
16
views
RSEM not giving .genes.results and isoforms.results ; Plase check if you provide correct parameters/options for the pipeline!
genomics
transcriptome
rsem
ngs
55 minutes ago by
kat.bi
• 0
0
votes
1
reply
29
views
how to create a loop in R
R
lm
loop
updated 1 hour ago by
Nicolas Rosewick
10k • written 1 hour ago by
mthm
▴ 50
0
votes
2
replies
43
views
BED files
BED
NGS
Chromosomes
updated 1 hour ago by
Alex Reynolds
35k • written 2 hours ago by
adarsh_pp
▴ 30
0
votes
0
replies
17
views
How the first sequencing product removed in pair end sequencing
NGS
RNA-seq
WGS
sequence
1 hour ago by
octpus616
▴ 80
0
votes
2
replies
128
views
Saving the output of LD pruning from SNPRelate package as a new GDS file
LD-pruning
SNPRelate
3 hours ago by
Patrick
• 0
0
votes
2
replies
422
views
Average Coverage after Assembly (Spades)
coverage
average
assembly
updated 3 hours ago by
taniapsduarte
• 0 • written 13 months ago by
davidmaimoun
▴ 50
762
votes
162
replies
123k
views
105 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 6 weeks ago by
Biostar
2.0k • written 6.8 years ago by
Istvan Albert
98k
0
votes
4
replies
640
views
Can vg take MUMmer output as input?
vg
updated 5 hours ago by
Qi
• 0 • written 2.8 years ago by
ac2278
▴ 20
0
votes
0
replies
44
views
Bacterial Pangenome Analysis
Pathogenic
Prokka
Roary
Pangenome
bacteria
5 hours ago by
kirankumareripogu
▴ 10
2
votes
4
replies
1.8k
views
Samtools Failing to Install through Conda
samtools
conda
updated 8 hours ago by
hukai916
▴ 10 • written 17 months ago by
jjp55
▴ 20
0
votes
1
reply
77
views
Violin plot (Monocle 3) - Troubleshooting
Monocle3
updated 1 hour ago by
fracarb8
★ 1.2k • written 11 hours ago by
sharic0010
• 0
3
votes
7
replies
263
views
Should I Learn Docker to Run Command Line Bioinformatics Tool?
Docker
updated 11 hours ago by
Yogi
▴ 10 • written 18 hours ago by
arriyaz.nstu
▴ 30
0
votes
1
reply
95
views
GO analysis after DESeq2
GO
updated 12 hours ago by
Ram
40k • written 12 hours ago by
oduduabasi.isaiah
• 0
0
votes
2
replies
117
views
Program for Overlapping DMRs (Differentially Methylated Regions) Between Groups
methylation
DMR
updated 3 hours ago by
Basti
★ 1.7k • written 13 hours ago by
epianalysis
• 0
0
votes
0
replies
63
views
News:
New NCBI Datasets APIs to Replace Old Ones
NCBI
API
Datasets
14 hours ago by
PeterC_NCBI
▴ 330
1
vote
3
replies
175
views
miRDeep2 - identifying miRNAs from deep sequencing data
microRNA
miRDeep2
updated 13 hours ago by
Ram
40k • written 15 hours ago by
Hasan
• 0
1
vote
4
replies
139
views
Unable to build applet in DNAnexus, .jar file not found
dnanexus
applet
updated 15 hours ago by
LChart
3.3k • written 19 hours ago by
_quantum_girl_
▴ 10
1
vote
4
replies
138
views
geom_signif() uses t-test to compare between more than 3 groups... Isn't this wrong?
ggplot2
ANOVA
t-test
10 minutes ago by
RM123
▴ 10
0
votes
1
reply
80
views
Download an example of fully-imputed VCF files ?
VCF
impute
updated 2 hours ago by
barslmn
★ 1.8k • written 16 hours ago by
Ben
• 0
0
votes
1
reply
115
views
How to find the most representative protein data base ID for your protein?
modelling
protein
database
updated 15 hours ago by
GenoMax
134k • written 22 hours ago by
amy__
▴ 150
0
votes
2
replies
136
views
Visualize where kmers are on a reference genome
kmer
visualize
updated 17 hours ago by
Alex Reynolds
35k • written 19 hours ago by
Carrie
• 0
5
votes
6
replies
238
views
6 follow
Filter human transcription factors
transcription-factor
RNA-seq
updated 1 hour ago by
Alex Reynolds
35k • written 17 hours ago by
Chris
▴ 180
2
votes
5
replies
182
views
obtaining circular RNAs' sequences from circBase
circular-RNA
updated 30 minutes ago by
Barry Digby
★ 1.2k • written 19 hours ago by
aminijavad4
▴ 10
0
votes
0
replies
67
views
How to annotate BED for tissue expression?
BED
annotation
18 hours ago by
Fabio_bie88
• 0
2
votes
0
replies
88
views
Job:
Human Genomics Team Leader
ebi
ensembl
embl
genomics
18 hours ago by
Ben_Ensembl
★ 2.3k
0
votes
1
reply
1.7k
views
error when running local chlorop1.1
chlorop
updated 19 hours ago by
Ram
40k • written 7.3 years ago by
gerrychang1985
▴ 40
0
votes
1
reply
96
views
How to determine the total count for each gene in lymphotype B
scRNAseq
Seurat
updated 19 hours ago by
fracarb8
★ 1.2k • written 20 hours ago by
dalibenam64
• 0
3
votes
15
replies
1.8k
views
9 follow
Help writing code for a question on my homework
biopython
updated 20 hours ago by
Andreas
• 0 • written 2.4 years ago by
hannahcheyenna
• 0
1
vote
1
reply
192
views
bedGraph for Coverage of Insert from Paired-End Data?
genome
awk
coverage
bed
paired-end
updated 20 hours ago by
shelkmike
▴ 980 • written 3 days ago by
vanbelj
▴ 40
0
votes
5
replies
138
views
gene correlations in between two groups
gene-expression
correlation
updated 33 minutes ago by
ATpoint
76k • written 21 hours ago by
edus_bioinfo
▴ 40
0
votes
1
reply
86
views
Running Ibex on both BCR chains?
BCR
ibex
single-cell
updated 19 hours ago by
Ram
40k • written 21 hours ago by
actinia94
• 0
1
vote
5
replies
270
views
Calculation of TMB on gene level
genomics
updated 3 hours ago by
Zhenyu Zhang
▴ 980 • written 22 hours ago by
smrutimayipanda
▴ 20
0
votes
0
replies
76
views
Spike-in normalization in ATAC-Seq with DiffBind
ATAC-Seq
spike-in
DiffBind
23 hours ago by
frueher
• 0
0
votes
1
reply
212
views
News:
LAST CALL: Online Course - A Practical Introduction to NGS Data Analysis - October 23-25, 2023
DNA-seq
Workshop
RNA-seq
23 hours ago by
David Langenberger
10k
1
vote
2
replies
125
views
Is it normal if regress out the cell cycle effects but the DEGs are quite the similar (no big changes)
regress_out
Cell_cycle
Seurat
21 hours ago by
alwayshope
▴ 30
1
vote
8
replies
289
views
how to identify uniq genes between two gff files.
Genes
Uniq
Annotation
GFF
updated 14 hours ago by
Juke34
8.2k • written 1 day ago by
nikhil
▴ 20
1
vote
3
replies
308
views
I have performed Trimmomatic run for adapter removal. QC report shows drop in the reads and presence of overrepresented sequences. Seeking help!
NGS
bioinformatics
illumina
WGS
updated 16 hours ago by
swbarnes2
13k • written 1 day ago by
Vijith
▴ 30
0
votes
0
replies
92
views
filtering variants in a Strelka2 VCF file based on AD and AF
Filter
VCF
1 day ago by
Bogdan
★ 1.4k
5
votes
4
replies
252
views
Low Alignment rate
alignment
low_alignment_rate
Bowtie2
14 hours ago by
Mehwish
• 0
2
votes
4
replies
222
views
Integrated Seurat object change name of the two conditions
R
integrated
Seurat
17 hours ago by
camillab.
▴ 130
0
votes
4
replies
300
views
Hugo_Symbol to Entrez ID
hugo
bioinformatics
entrez
ids
symbols
updated 1 day ago by
Kevin Blighe
86k • written 3 days ago by
shakyaram079
• 0
2
votes
5
replies
264
views
How to change from gene_id to GeneID/EntrezID using R
identifiers
Deseq2
GeneID
updated 23 hours ago by
Kevin Blighe
86k • written 2 days ago by
Nicolas
• 0
0
votes
4
replies
706
views
Is there a way to get a list of all homogygous sites for each sample with plink (regardless if they are in a run)
plink
updated 1 day ago by
chrchang523
10k • written 16 days ago by
curious
▴ 730
1
vote
4
replies
222
views
How to sort cd-hit-est cluster file
sort
cd-hit-est
12 hours ago by
Mo
▴ 40
1
vote
4
replies
217
views
Enrichment of mitochondrial and ribosomal pathways - an artifact?
Pathway
Mitochondria
Ribosome
scRNA-seq
Enrichment
updated 9 hours ago by
LauferVA
3.7k • written 1 day ago by
omer.shomrat
• 0
13
votes
10
replies
604
views
8 follow
scRNAseq Differential expression analysis
scRNA-seq
Differential-Expression
Seurat
updated 1 day ago by
ATpoint
76k • written 4 days ago by
MVJ
▴ 10
112,646 results • Page
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Comment: Quantification after transcriptome assembly with Trinity
Snakemake: output folder a as dependency to a different rule
A: Snakemake: output folder a as dependency to a different rule
A: In Seurat, How Do nCount_RNA Differ from nFeature_RNA?
How to identify 16s sequences from binning data(contigs)?
geom_signif() uses t-test to compare between more than 3 groups... Isn't this wrong?
Answer: Filter transcription factors
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Recent Replies
Answer: Gene enrichment analysis of prokaryotes gene
by
dthorbur
▴ 550
[Here](https://github.com/golden75/prokaryote_RNASeq) is a tutorial on how to use the R package DESeq2 for prokaryotic RNAseq analyses. …
Comment: Read block operation failed with BAM file
by
John Marshall
3.0k
Indeed, though it is a seek issue when accessing files over HTTP and other network protocols. So, unless there's something you didn't menti…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr
by
RM123
▴ 10
Thank you for your help. I am comparing 4 groups, but as I have gene expression data I have a considerable number of boxplots to make. I fo…
Comment: gene correlations in between two groups
by
ATpoint
76k
And how should I know this? I cannot read minds, nor see your screen, data or anything. Please ask a good question with necessary details. …
Comment: gene correlations in between two groups
by
edus_bioinfo
▴ 40
Thanks. But they are already analyzed. Afaik it analyzes raw data. In my dataset for each gene there is score. I want to interpret the data…
Answer: GWAS phenotype
by
dthorbur
▴ 550
Hello again. Yes, you can conduct GWAS using binary trait data, but it comes with a whole suite of complications. See [this](https://ww…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr
by
RM123
▴ 10
Hello Dariober, That seems like a good solution, however I'm pretty new to R. Could you tell me how I can do that?
Comment: how to create a loop in R
by
Nicolas Rosewick
10k
Not really a bioinformatics related question. Start by looking at R tutorial, there is plenty of them online e.g. : https://www.statmethods…
Comment: Violin plot (Monocle 3) - Troubleshooting
by
fracarb8
★ 1.2k
You did not add the screenshot.
Answer: BED files
by
Alex Reynolds
35k
Generically via `bedmap`: ``` bedmap --echo --echo-map --count exome.bed annotations.bed > answer.bed ``` The `annotations.bed` fil…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr
by
dariober
14k
It seems to me that anova followed by HSD is a more sensible approach than applying independent t-tests. Granted this is the first time I s…
Comment: BED files
by
barslmn
★ 1.8k
I am guessing you want the annotation files. https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/
Comment: Filter human transcription factors
by
Alex Reynolds
35k
Curious how redundant these TFs are. Jeff Vierstra has done some analysis on this to simplify model sets: https://www.vierstra.org/resource…
Comment: Read block operation failed with BAM file
by
Alex Reynolds
35k
https://github.com/samtools/htslib/pull/1676 patches a seek issue in `htslib` (upon which `samtools` and `pysam` depend)
Comment: Merging the filename with tsv files for master file
by
barslmn
★ 1.8k
Could you add samples from your files and your expected output.
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