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39 results • Page
1 of 1
Sort: Votes
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Replies
13
votes
10
replies
561
views
8 follow
scRNAseq Differential expression analysis
scRNA-seq
Differential-Expression
Seurat
updated 10 hours ago by
ATpoint
76k • written 3 days ago by
MVJ
▴ 10
4
votes
8
replies
537
views
Assistance with Fungal Genome Annotation Using Maker and BLAST
gff3
fasta
maker
xml
blastp
10 hours ago by
Edoardo
• 0
3
votes
15
replies
1.8k
views
9 follow
Help writing code for a question on my homework
biopython
updated 3 hours ago by
Andreas
• 0 • written 2.4 years ago by
hannahcheyenna
• 0
3
votes
4
replies
238
views
Dotplot : how to self-define the range of legend
analysis
seq
RNA
updated 3 hours ago by
GenoMax
134k • written 1 day ago by
Xuhao
• 0
3
votes
4
replies
42
views
Filter human transcription factors
transcription-factor
RNA-seq
31 minutes ago by
Chris
▴ 180
2
votes
5
replies
1.8k
views
How to make alpha diversity boxplot?
alpha_diversity
taxa
ASV
box_plot
shannon
updated 8 hours ago by
yeah
• 0 • written 10 months ago by
Amr
▴ 140
2
votes
1
reply
206
views
News:
Successful NCBI NIAID Codeathon on VCF Files in SARS-CoV-2 Genomics
NCBI
Codeathon
updated 22 hours ago by
chrchang523
10k • written 3 days ago by
PeterC_NCBI
▴ 330
2
votes
5
replies
235
views
How to change from gene_id to GeneID/EntrezID using R
identifiers
Deseq2
GeneID
updated 6 hours ago by
Kevin Blighe
86k • written 1 day ago by
Nicolas
• 0
2
votes
4
replies
131
views
Integrated Seurat object change name of the two conditions
R
integrated
Seurat
45 minutes ago by
camillab.
▴ 130
2
votes
2
replies
113
views
Low Alignment rate
alignment
low_alignment_rate
Bowtie2
updated 1 hour ago by
biofalconch
▴ 970 • written 18 hours ago by
Mehwish
• 0
2
votes
5
replies
47
views
Should I Learn Docker to Run Command Line Bioinformatics Tool?
Docker
updated 33 minutes ago by
ATpoint
76k • written 1 hour ago by
arriyaz.nstu
▴ 30
1
vote
2
replies
265
views
Restricting vcf entries based on ID length
bcftools
vcf
vcftools
updated 23 hours ago by
chrchang523
10k • written 17 days ago by
ethan.kreuzer
• 0
1
vote
4
replies
241
views
Hisat2 index and alignment question
ubuntu
rna-seq
index
hisat2
12 hours ago by
Athena
• 0
1
vote
1
reply
979
views
SCENIC-openloom not working
sc-rna
SCENIC
sequencing
updated 8 hours ago by
kyriakds
• 0 • written 2.0 years ago by
Lekshmy
▴ 10
1
vote
3
replies
251
views
How to find out what adapters to remove after FastQC of RNAseq data?
Trimmomatic
FastQC
NGS
RNA-seq
5 hours ago by
ella
• 0
1
vote
3
replies
186
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 4 hours ago by
GenoMax
134k • written 10 hours ago by
Vijith
▴ 30
1
vote
2
replies
91
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
4 hours ago by
alwayshope
▴ 30
1
vote
1
reply
162
views
bedGraph for Coverage of Insert from Paired-End Data?
genome
awk
coverage
bed
paired-end
updated 3 hours ago by
shelkmike
▴ 980 • written 2 days ago by
vanbelj
▴ 40
1
vote
3
replies
144
views
Enrichment of mitochondrial and ribosomal pathways - an artifact?
Pathway
Mitochondria
Ribosome
scRNA-seq
Enrichment
updated 2 hours ago by
ATpoint
76k • written 1 day ago by
omer.shomrat
• 0
1
vote
0
replies
19
views
Job:
Human Genomics Team Leader
ebi
ensembl
embl
genomics
1 hour ago by
Ben_Ensembl
★ 2.3k
0
votes
1
reply
190
views
News:
LAST CALL: Online Course - A Practical Introduction to NGS Data Analysis - October 23-25, 2023
DNA-seq
Workshop
RNA-seq
6 hours ago by
David Langenberger
10k
0
votes
2
replies
44
views
Visualize where kmers are on a reference genome
kmer
visualize
updated 51 minutes ago by
Alex Reynolds
35k • written 2 hours ago by
Carrie
• 0
0
votes
3
replies
246
views
how to extract unique snps in a vcf file by comparing with multiple vcf files
bcftools
SNP
GATK
VCF
updated 9 hours ago by
Pierre Lindenbaum
157k • written 4 weeks ago by
nikhil
▴ 10
0
votes
5
replies
414
views
genome data downloads for various strains
gisaid
hass-marr
updated 2 hours ago by
Ram
40k • written 4 days ago by
iftikharmaryam123
• 0
0
votes
1
reply
1.6k
views
error when running local chlorop1.1
chlorop
updated 2 hours ago by
Ram
40k • written 7.3 years ago by
gerrychang1985
▴ 40
0
votes
1
reply
59
views
gene correlations in between two groups
gene-expression
correlation
updated 2 hours ago by
Ram
40k • written 4 hours ago by
edus_bioinfo
▴ 40
0
votes
1
reply
49
views
Running Ibex on both BCR chains?
BCR
ibex
single-cell
updated 2 hours ago by
Ram
40k • written 4 hours ago by
actinia94
• 0
0
votes
1
reply
52
views
How to determine the total count for each gene in lymphotype B
scRNAseq
Seurat
updated 2 hours ago by
fracarb8
★ 1.2k • written 3 hours ago by
dalibenam64
• 0
0
votes
3
replies
43
views
Unable to build applet in DNAnexus, .jar file not found
dnanexus
applet
updated 2 hours ago by
Ram
40k • written 2 hours ago by
_quantum_girl_
▴ 10
0
votes
4
replies
273
views
Hugo_Symbol to Entrez ID
hugo
bioinformatics
entrez
ids
symbols
updated 21 hours ago by
Kevin Blighe
86k • written 2 days ago by
shakyaram079
• 0
0
votes
4
replies
681
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 22 hours ago by
chrchang523
10k • written 16 days ago by
curious
▴ 730
0
votes
0
replies
11
views
How to annotate BED for tissue expression?
BED
annotation
1 hour ago by
Fabio_bie88
• 0
0
votes
2
replies
37
views
obtaining circular RNAs' sequences from circBase
circular-RNA
updated 1 hour ago by
Barry Digby
★ 1.2k • written 2 hours ago by
aminijavad4
▴ 10
0
votes
0
replies
41
views
Spike-in normalization in ATAC-Seq with DiffBind
ATAC-Seq
spike-in
DiffBind
6 hours ago by
frueher
• 0
0
votes
0
replies
40
views
How to find the most representative protein data base ID for your protein?
modelling
protein
database
5 hours ago by
amy__
▴ 150
0
votes
0
replies
64
views
filtering variants in a Strelka2 VCF file based on AD and AF
Filter
VCF
15 hours ago by
Bogdan
★ 1.4k
0
votes
7
replies
188
views
how to identify uniq genes between two gff files.
Genes
Uniq
Annotation
GFF
1 hour ago by
nikhil
▴ 10
0
votes
7
replies
451
views
Highly inflated p-values in GWAS by regenie
regenie
plink
gwas
19 hours ago by
cwwong13
▴ 20
0
votes
2
replies
95
views
Calculation of TMB on gene level
genomics
updated 3 hours ago by
ATpoint
76k • written 5 hours ago by
smrutimayipanda
▴ 20
39 results • Page
1 of 1
Recent Votes
Comment: Low Alignment rate
Answer: Filter transcription factors
Answer: Filter transcription factors
Answer: Filter transcription factors
Comment: Integrated Seurat object change name of the two conditions
Comment: Integrated Seurat object change name of the two conditions
Concatenating fastq.gz files across lanes
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Recent Replies
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool?
by
ATpoint
76k
Never tried, so idk. Why wouldn't it support it?
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool?
by
ATpoint
76k
I never tried conda images but since `mamba > conda` I guess mambaforge is better.
Comment: Filter human transcription factors
by
Chris
▴ 180
Thank you so much!
Comment: Filter human transcription factors
by
Chris
▴ 180
Yes, I do GO and GSEA to get pathway. I download the background gene at https://www.gsea-msigdb.org/gsea/msigdb/human/collections.jsp#C3 Th…
Answer: Visualize where kmers are on a reference genome
by
Alex Reynolds
35k
Make a bigBed file: https://www.biostars.org/p/9546293/ Then view it on the UCSC Genome Browser: http://genome.ucsc.edu/goldenPath/help/…
Comment: Integrated Seurat object change name of the two conditions
by
camillab.
▴ 130
great! thank you very much!
Answer: Filter transcription factors
by
jared.andrews07
★ 15k
[This database](http://humantfs.ccbr.utoronto.ca/download.php) has been the best I've found.
Comment: Filter transcription factors
by
Ram
40k
What have you tried? Have you looked at GO annotations?
Comment: how to identify uniq genes between two gff files.
by
nikhil
▴ 10
yes @juke34 , I tried agat_sp_compare_two_annotations.pl for both gff files and got comparative output in table format. Thank you very muc…
Comment: Integrated Seurat object change name of the two conditions
by
Amitm
★ 2.2k
Yes, its similar structure. This snippet should add a new metadata column "sample.New" with what you want to do # Assuming a seurat obj. c…
Comment: Low Alignment rate
by
biofalconch
▴ 970
Yeap, you can sample your reads with `seqtk` like this: seqtk sample -s100 read2.fq 100 > Sample.fq Take a couple and run them throug…
Answer: obtaining circular RNAs' sequences from circBase
by
Barry Digby
★ 1.2k
You won't find them on circBase. circAtlas has the mature spliced sequence available. You can [search for circRNAs](https://ngdc.cncb.a…
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool?
by
Ram
40k
\#TIL mambaforge - better than continuum's conda images I'm guessing?
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool?
by
arriyaz.nstu
▴ 30
If the laptop doesn't support WSL2, then will the Docker (with linux) work?
Comment: Integrated Seurat object change name of the two conditions
by
camillab.
▴ 130
thanks but my metadata looks different from yours. Will it work even there are not the same "structure"? or…
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