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212 results • Page
1 of 5
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0
votes
0
replies
4
views
How to find the most representative protein data base ID for your protein?
modelling
protein
database
13 minutes ago by
amy__
▴ 150
0
votes
0
replies
7
views
Calculation of TMB on gene level
genomics
31 minutes ago by
smrutimayipanda
▴ 20
0
votes
0
replies
7
views
Spike-in normalization in ATAC-Seq with DiffBind
ATAC-Seq
spike-in
DiffBind
47 minutes ago by
frueher
• 0
0
votes
1
reply
152
views
News:
LAST CALL: Online Course - A Practical Introduction to NGS Data Analysis - October 23-25, 2023
DNA-seq
Workshop
RNA-seq
1 hour ago by
David Langenberger
10k
0
votes
0
replies
15
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
1 hour ago by
alwayshope
▴ 30
0
votes
6
replies
134
views
how to identify uniq genes between two gff files.
Genes
Uniq
Annotation
GFF
updated 1 hour ago by
Juke34
8.2k • written 4 hours ago by
nikhil
▴ 10
0
votes
0
replies
28
views
How to create applets in DNAnexus platform?
dnanexus
applet
2 hours ago by
_quantum_girl_
▴ 10
1
vote
2
replies
121
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
3 hours ago by
Vijith
▴ 30
0
votes
0
replies
53
views
filtering variants in a Strelka2 VCF file based on AD and AF
Filter
VCF
9 hours ago by
Bogdan
★ 1.4k
1
vote
1
reply
95
views
Low Alignment rate
alignment
low_alignment_rate
Bowtie2
updated 10 hours ago by
dsull
★ 4.7k • written 13 hours ago by
Mehwish
• 0
0
votes
1
reply
105
views
Integrated Seurat object change name of the two conditions
R
integrated
Seurat
updated 12 hours ago by
Amitm
★ 2.2k • written 15 hours ago by
camillab.
▴ 130
0
votes
4
replies
264
views
Hugo_Symbol to Entrez ID
hugo
bioinformatics
entrez
ids
symbols
updated 16 hours ago by
Kevin Blighe
86k • written 2 days ago by
shakyaram079
• 0
2
votes
5
replies
225
views
How to change from gene_id to GeneID/EntrezID using R
identifiers
Deseq2
GeneID
updated 1 hour ago by
Kevin Blighe
86k • written 1 day ago by
Nicolas
• 0
0
votes
4
replies
673
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 17 hours ago by
chrchang523
10k • written 15 days ago by
curious
▴ 730
0
votes
3
replies
146
views
How to sort cd-hit-est cluster file
sort
cd-hit-est
updated 19 hours ago by
Pierre Lindenbaum
157k • written 21 hours ago by
Mo
▴ 40
0
votes
1
reply
89
views
Enrichment of mitochondrial and ribosomal pathways - an artifact?
Pathway
Mitochondria
Ribosome
scRNA-seq
Enrichment
updated 1 hour ago by
ATpoint
76k • written 21 hours ago by
omer.shomrat
• 0
13
votes
10
replies
541
views
8 follow
scRNAseq Differential expression analysis
scRNA-seq
Differential-Expression
Seurat
updated 4 hours ago by
ATpoint
76k • written 3 days ago by
MVJ
▴ 10
2
votes
4
replies
224
views
Dotplot : how to self-define the range of legend
RNA
seq
analysis
8 hours ago by
Xuhao
• 0
0
votes
0
replies
73
views
News:
RADseq data analysis course
RADseq
Phylogenomics
Bioinformatics
Populationgenomics
Stacks
1 day ago by
carlopecoraro2
★ 2.3k
3
votes
2
replies
323
views
How to create structural variants ground truth for alignment of two long-read genome assemblies?
yeast
assembly
structural-variation
SV-callers
1 day ago by
Thomas
▴ 20
0
votes
0
replies
132
views
Merging the filename with tsv files for master file
genomics
1 day ago by
smrutimayipanda
▴ 20
1
vote
4
replies
227
views
Hisat2 index and alignment question
ubuntu
rna-seq
index
hisat2
7 hours ago by
Athena
• 0
2
votes
4
replies
295
views
Ties in reranked list
fgsea
GSEA
1 day ago by
Hamza
• 0
1
vote
4
replies
292
views
Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempting To Use CuffDiff
CuffDiff
Bash
Cufflinks
1 day ago by
Y
• 0
0
votes
0
replies
108
views
My rMATS output file is not showing gene symbols and only XLOC gene ID are being shown.
rMATS
rMATS-turbo
1 day ago by
Nipan
• 0
2
votes
4
replies
234
views
Using STAR aligner to build index of hg38
hg38
STAR
alignment
RNAseq
index
1 day ago by
Grace
• 0
0
votes
0
replies
125
views
Convert RNASeq V2 data in cBioPortal having RSEM normalized results to TPM values
bioinformatics
TPM
RNASeqV2
cbioportal
RSEM
updated 1 day ago by
4galaxy77
2.8k • written 2 days ago by
shakyaram079
• 0
0
votes
2
replies
236
views
Modify the code to take most abundant reads from a cluster and process it.
cd-hit-est
clustering
1 day ago by
Mo
▴ 40
0
votes
1
reply
168
views
Understanding TCGA barcodes with dot in the fieldname
tcga
updated 2 days ago by
Ram
40k • written 2 days ago by
Tahsin
• 0
0
votes
0
replies
133
views
Compare peaks between clusters in sc-ATAC
Peak-Calling
Epigenome
scATAC-seq
updated 2 days ago by
Ram
40k • written 2 days ago by
Ahmed.waraky
▴ 10
0
votes
0
replies
131
views
bedGraph for Coverage of Insert from Paired-End Data?
genome
awk
coverage
bed
paired-end
2 days ago by
vanbelj
▴ 40
1
vote
3
replies
336
views
How to DESeq2 using miRNA data obtained using TCGAbiolinks
R
TCGAbiolinks
DESeq2
TCGA
updated 2 days ago by
Zhenyu Zhang
▴ 980 • written 4 days ago by
Mo
• 0
0
votes
7
replies
440
views
Highly inflated p-values in GWAS by regenie
regenie
plink
gwas
14 hours ago by
cwwong13
▴ 20
1
vote
3
replies
195
views
How to find out what adapters to remove after FastQC of RNAseq data?
Trimmomatic
FastQC
NGS
RNA-seq
just now by
ella
• 0
2
votes
5
replies
299
views
Trimmomatic .jar not included anymore?
trimmomatic
ubuntu
linux
updated 2 days ago by
petebio
▴ 100 • written 2 days ago by
Emily
▴ 30
0
votes
1
reply
167
views
News:
EMBL-EBI virtual course | Introduction to RNA-seq and functional interpretation
RNA-seq
updated 2 days ago by
Ram
40k • written 2 days ago by
Rebecca
• 0
0
votes
4
replies
289
views
Weirdness in annotation (missing allele frequencies)
allele-frequency
gnomad
annovar
updated 1 day ago by
Jeremy Leipzig
21k • written 2 days ago by
Can Abdullah
• 0
1
vote
3
replies
202
views
Finding sequences in unannotated genomes using reference coordinates
consensus
VCF
updated 2 days ago by
Ram
40k • written 2 days ago by
Prangan
▴ 20
0
votes
1
reply
194
views
High amount of intronic/intergenic reads in SMARTer stranded total bulk RNAseq
RNA-seq
DNA
SMARTer
updated 2 days ago by
Ram
40k • written 2 days ago by
Mat
▴ 60
2
votes
2
replies
232
views
How to check RNAseq support for annotated genes?
gene
RNA-seq
annotation
updated 2 days ago by
Michael
53k • written 3 days ago by
BioinfoBee
• 0
0
votes
0
replies
262
views
Why dbConnect GEOmetadb_demo.sqlite shows some information while dbConnect GEOmetadb.sqlite shows no information
R
GEO
GEOmetadb
updated 2 days ago by
Pierre Lindenbaum
157k • written 3 days ago by
nonaddldy
▴ 10
1
vote
0
replies
155
views
News:
Online Training - Bioinformatics Pipeline Development with Nextflow (November 15-17, 2023)
nextflow
automation
pipeline
development
3 days ago by
David Langenberger
10k
0
votes
3
replies
264
views
ATAC-seq troubleshoot - Just Noise
ATAC-seq
updated 2 days ago by
Ram
40k • written 3 days ago by
vk
▴ 40
1
vote
1
reply
202
views
Simulate short-read RNA-seq data from long-read RNA-seq data
polyester
single-cell
simulation
short-read
long-read
updated 3 days ago by
Mensur Dlakic
★ 24k • written 3 days ago by
rhonddaskl
• 0
0
votes
0
replies
152
views
Gene enrichment analysis of prokaryotes gene
prokaryotes
GO
enrichment
DEG
3 days ago by
Genta
• 0
4
votes
4
replies
398
views
DESeq2 analysis using two featureCounts generated from different studies
RNA-seq
DESeq2
3 days ago by
abedkurdi10
▴ 190
3
votes
4
replies
325
views
Filtering VCF to divide with equal sizes
bcftools
vcf
updated 3 days ago by
Ram
40k • written 3 days ago by
avelarbio46
▴ 30
0
votes
0
replies
162
views
High pvalues when using clusterProfiler for seurat
clusterProfiler
3 days ago by
Ahmed
• 0
5
votes
2
replies
238
views
kallisto normalized TPM values without bootstraps
tpm
cibersort
sleuth
kallisto
RNA-seq
2 days ago by
butterman16
▴ 20
5
votes
7
replies
402
views
Salmon index not progressing
salmon
updated 2 days ago by
Michael
53k • written 3 days ago by
camillab.
▴ 130
212 results • Page
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Recent Votes
Comment: How to create structural variants ground truth for alignment of two long-read ge
Comment: Low Alignment rate
Answer: How to retrieve LoF and missense variants in WES data?
Answer: I have performed Trimmomatic run for adapter removal. QC report shows drop in th
Comment: Assistance with Fungal Genome Annotation Using Maker and BLAST
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
Comment: Hisat2 index and alignment question
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Recent Replies
Comment: Enrichment of mitochondrial and ribosomal pathways - an artifact?
by
ATpoint
76k
Generally these genes are highly expressed, so there would be some sort of a power bias. How do you do the DE analysis? Any cutoffs on mini…
Answer: Online Course - A Practical Introduction to NGS Data Analysis - October 23-25, 2
by
David Langenberger
10k
:: LAST CALL :: Apply now, if you want to join this online workshop!
Answer: how to identify uniq genes between two gff files.
by
Juke34
8.2k
You can run `agat_sp_compare_two_annotations.pl` from [AGAT][1], you should get the information you are looking for. This method allow to c…
Comment: How to find out what adapters to remove after FastQC of RNAseq data?
by
ella
• 0
Thank you for the fast help, I have the BBMap suite installed anyways and will try it out :)
Comment: How to make alpha diversity boxplot?
by
yeah
• 0
thanks a lot! can't believe that is so simple
Comment: how to identify uniq genes between two gff files.
by
nikhil
▴ 10
yes got it, thank you very much.
Comment: SCENIC-openloom not working
by
kyriakds
• 0
Hello, Did you find a solution in the end?
Comment: I have performed Trimmomatic run for adapter removal. QC report shows drop in th
by
Vijith
▴ 30
@swbarnes2, thanks for the response, by the way, can you tell me why/ how this happens during the sequencing process, and if it could negat…
Comment: how to identify uniq genes between two gff files.
by
Pierre Lindenbaum
157k
> can you explain this ?? yes. you should use options like `-u` . > Write original A entry once if any overlaps found in B. In other word…
Comment: how to extract unique snps in a vcf file by comparing with multiple vcf files
by
Pierre Lindenbaum
157k
so validate the answer to close the question please (Green tick on the left).
Comment: how to identify uniq genes between two gff files.
by
nikhil
▴ 10
hi Pierre Linderbaum, after extracting genes, I have 5846 genes in afile.bed and 4456 genes in bfile.bed , while using bedtools intersec…
Comment: how to extract unique snps in a vcf file by comparing with multiple vcf files
by
nikhil
▴ 10
thank you, bcftools isec is working well.
Comment: how to identify uniq genes between two gff files.
by
Pierre Lindenbaum
157k
please, comment or validate the answers to your previous questions: https://www.biostars.org/p/9573151/#9573158 ; https://www.biostars.org/…
Answer: how to identify uniq genes between two gff files.
by
Pierre Lindenbaum
157k
extract genes (e.g: awk '($3=="gene") {printf("%s\t%d\t%s\n",$1;int($4)-1,$5);}' ) from both files n sort, and use bedtools intersect with…
Answer: I have performed Trimmomatic run for adapter removal. QC report shows drop in th
by
swbarnes2
13k
G is the letter you get if there is no fluorescence. 75% of your reads have a lot of G. I don't think this run worked.
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