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477 results • Page
1 of 10
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Rank
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0
votes
0
replies
1
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Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
just now by
rustykb
▴ 20
1
vote
2
replies
38
views
Generating mpileup file using samtools
mpileup
samtools
updated 10 minutes ago by
ATpoint
82k • written 2 hours ago by
Ruqaiya
• 0
0
votes
0
replies
49
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
4 hours ago by
Vijith
▴ 30
0
votes
0
replies
53
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
6 hours ago by
Jeyong
• 0
0
votes
0
replies
51
views
Empty table plot using plotGseaTable()
FGSEA
13 hours ago by
Chris
▴ 260
1
vote
2
replies
121
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
14 hours ago by
Maverick
▴ 10
3
votes
8
replies
6.5k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 16 hours ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
109
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
16 hours ago by
dtnondorf
• 0
0
votes
1
reply
131
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 8 hours ago by
Chris Dean
▴ 390 • written 17 hours ago by
sovrappensiero
▴ 90
2
votes
6
replies
249
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
10 hours ago by
Qroid
▴ 40
0
votes
1
reply
96
views
Provean help
variant
Provean
updated 15 hours ago by
Mensur Dlakic
★ 27k • written 19 hours ago by
Arun Sai Kumar
• 0
0
votes
0
replies
71
views
Use of annotation of integrated Seurat object in single sample
Seurat
1 day ago by
Bine
▴ 60
0
votes
1
reply
194
views
Subsetting and merging back Seurat Object brings different results
Seurat
22 hours ago by
Bine
▴ 60
1
vote
1
reply
116
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 19 hours ago by
Ram
43k • written 1 day ago by
marco.barr
▴ 90
0
votes
0
replies
69
views
edgeR contrasts for analysis of reciprocal hybrid crosses - averaging, pooling, and comparing groups
edgeR
1 day ago by
Rhiannon
• 0
0
votes
1
reply
112
views
How to perform single cell multimodal integration using Seurat for Geo datasets
multimodal-analysis
single-cell
updated 16 hours ago by
Ram
43k • written 1 day ago by
nithya
• 0
0
votes
0
replies
79
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
1 day ago by
Vijith
▴ 30
0
votes
0
replies
78
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
1 day ago by
James
▴ 10
0
votes
1
reply
567
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 1 day ago by
mdav
• 0 • written 18 months ago by
Zoe
• 0
1
vote
3
replies
178
views
Odd alignment question/finding
Alignment
updated 1 hour ago by
barslmn
★ 2.1k • written 1 day ago by
poordumbsillyidiot
• 0
0
votes
1
reply
185
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 1 day ago by
GenoMax
142k • written 1 day ago by
mgranada3
▴ 30
0
votes
0
replies
81
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
1 day ago by
meck
• 0
0
votes
0
replies
111
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 1 day ago by
Ram
43k • written 1 day ago by
Oscar
▴ 10
0
votes
1
reply
130
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 1 day ago by
Ram
43k • written 1 day ago by
ernestine.kubi
• 0
0
votes
0
replies
99
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
1 day ago by
VITALA
• 0
1
vote
2
replies
233
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
1 day ago by
rianna.collins
• 0
0
votes
1
reply
170
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 2 days ago by
i.sudbery
19k • written 2 days ago by
Edmond
• 0
0
votes
0
replies
135
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
2 days ago by
O.rka
▴ 710
0
votes
1
reply
507
views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated 2 days ago by
Ram
43k • written 2 days ago by
Dr Huma Naz
• 0
0
votes
5
replies
340
views
Telescope issue
Telescope
RNA-seq
updated 1 day ago by
GenoMax
142k • written 2 days ago by
eleven11
• 0
1
vote
1
reply
217
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 2 days ago by
Ram
43k • written 2 days ago by
Jonathan Yoou
▴ 60
1
vote
2
replies
273
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
1 day ago by
Nafi
• 0
1
vote
3
replies
261
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 2 days ago by
GenoMax
142k • written 2 days ago by
jeffrey.maurer.informatics
• 0
0
votes
1
reply
169
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
updated 1 day ago by
Adam
▴ 30 • written 2 days ago by
Ahiad Chen Zion
• 0
0
votes
0
replies
122
views
barcode of TCR-sequencing
barcode
2 days ago by
yueli7
▴ 250
0
votes
0
replies
116
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 2 days ago by
Ram
43k • written 2 days ago by
Alexandros
• 0
0
votes
1
reply
157
views
unable to get feature count results
featureCounts
updated 2 days ago by
Ram
43k • written 3 days ago by
Ravita
• 0
0
votes
3
replies
262
views
KEGG Pathways
r
RNA-seq
updated 2 days ago by
Ram
43k • written 3 days ago by
Sudip
• 0
0
votes
0
replies
124
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
3 days ago by
Bine
▴ 60
0
votes
0
replies
123
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
3 days ago by
8armed
• 0
1
vote
2
replies
215
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 2 days ago by
Ram
43k • written 3 days ago by
Ravita
• 0
0
votes
0
replies
107
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
3 days ago by
Adyasha
• 0
0
votes
0
replies
110
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
3 days ago by
fanglujing
▴ 60
0
votes
0
replies
125
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
3 days ago by
Jacob
• 0
0
votes
1
reply
178
views
Differential Accessibility
DiffBind
updated 3 days ago by
Ram
43k • written 3 days ago by
Shloka
• 0
0
votes
3
replies
272
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 2 days ago by
GenoMax
142k • written 3 days ago by
kim
• 0
3
votes
7
replies
325
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
3 days ago by
salias
• 0
0
votes
0
replies
122
views
Using limma in methylation EM-seq?
EM-seq
methylation
3 days ago by
Lluís R.
★ 1.2k
0
votes
0
replies
121
views
Synteny analysis
bacterial
synteny
genome
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Namil
• 0
0
votes
4
replies
241
views
Genbank File Format
gbkformat
3 days ago by
alenew.am
• 0
477 results • Page
1 of 10
Recent Votes
Comment: Generating mpileup file using samtools
Answer: What analysis suitable to identify similarly expressed genes between two samples
Comment: What analysis suitable to identify similarly expressed genes between two samples
C: Split Fastq Files Into Chunks Of 1M Reads
Answer: How many reads for WGS Sequencing?
Answer: How many reads for WGS Sequencing?
Comment: How to Calulate Allele Frequency from a VCF File?
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Recent Awards •
All
Popular Question
to
ManuelDB
▴ 80
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rustykb
▴ 20
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sativus
▴ 20
Student
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Mariana
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Shicheng Guo
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Recent Replies
Comment: Generating mpileup file using samtools
by
ATpoint
82k
Seconding this. Apply current best practices (which is bcftools mpileup followed by something I forgot, see bcftools manual for variant cal…
Answer: Analysis of intronic reads included scRNA-seq data
by
ATpoint
82k
By default in CellRanger (lets assume you have 10x data processed with it) intronic reads are included. What you get in your matrix.mtx fil…
Comment: How does gene length effect the number of reads mapped
by
i.sudbery
19k
The number of reads for a gene is almost exactly linearly proportional to the length of the gene. In paired-end sequencing, we generally co…
Comment: What analysis suitable to identify similarly expressed genes between two samples
by
ATpoint
82k
Can you post your setup, so how many groups and their replication number? I can tell you by experience that you need even more replication …
Answer: DSEQ2 analysis
by
ATpoint
82k
The tool is called D**E**Seq2. Anyway, if your factor is `factor(conditions, levels = c("control", "mutant"))` then the first level is the …
Comment: Odd alignment question/finding
by
barslmn
★ 2.1k
Maybe it is caused by fastp. https://github.com/OpenGene/fastp/issues/506
Comment: Generating mpileup file using samtools
by
Joe
21k
It's been a long time since I did this sort of thing, but I have a vague recollection that the mpileup process was made simpler and/or roll…
Comment: Introduce SNPs on FASTA
by
Riccardo
▴ 10
Thank you very much for your answer!
Comment: how to split multi-fasta file into single fasta file named by header
by
rsieber
▴ 10
This is great also for multiline fastas
Comment: how to split multi-fasta file into single fasta file named by header
by
rsieber
▴ 10
This only works for the first line of sequences.
Answer: What purposes can TPM values be used for?
by
b.contreras.moreira
▴ 180
In case it helps: https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units
Comment: What analysis suitable to identify similarly expressed genes between two samples
by
alifafiq1
• 0
Thank you @AT point. I was planning to use DESeq2 and use the alternate hypothesis (lessAbs) too considering that is the only package that …
Comment: Does comparing two different groups to a common third group introduce bias in th
by
ATpoint
82k
Note that by basic algebra A vs C and B vs C is the same as A vs B, so you might rethink your analysis to answer your question in a much si…
Comment: RNAseq one control two conditions, shared and exclusive genes
by
Mohamed Abderrahmane
▴ 20
Yes, why not? If it works for you like that, bingo!
Answer: Does comparing two different groups to a common third group introduce bias in th
by
christopher medway
▴ 450
You are testing groups A and B to a common baseline (C) - I don't see that there is anything wrong with doing that. It is a fairly common a…
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