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47 results • Page
1 of 1
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Votes
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0
votes
0
replies
11
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
18 minutes ago by
rustykb
▴ 20
1
vote
1
reply
25
views
Analysis of intronic reads included scRNA-seq data
cell
single
updated 21 minutes ago by
ATpoint
82k • written 1 hour ago by
carolofharvest
▴ 10
0
votes
1
reply
24
views
DSEQ2 analysis
DSEQ2
logfoldchane
updated 1 hour ago by
ATpoint
82k • written 1 hour ago by
adi.gershon1
• 0
3
votes
4
replies
47
views
Generating mpileup file using samtools
mpileup
samtools
10 minutes ago by
Ruqaiya
• 0
0
votes
5
replies
196
views
6 follow
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 2 hours ago by
b.contreras.moreira
▴ 180 • written 20 hours ago by
JH
• 0
0
votes
3
replies
147
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 3 hours ago by
ATpoint
82k • written 13 hours ago by
Qi
• 0
0
votes
0
replies
36
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
4 hours ago by
Amos Bairoch
▴ 120
0
votes
0
replies
51
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
55
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
6 hours ago by
Jeyong
• 0
0
votes
2
replies
642
views
homer not configured properly
Homer
makeTagDirectory
updated 8 hours ago by
clairechung112
• 0 • written 23 months ago by
amahdi779
• 0
1
vote
3
replies
155
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 8 hours ago by
Alex Reynolds
35k • written 15 hours ago by
SJP
• 0
0
votes
0
replies
53
views
Empty table plot using plotGseaTable()
FGSEA
13 hours ago by
Chris
▴ 260
0
votes
1
reply
101
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 14 hours ago by
anovak
▴ 120 • written 18 hours ago by
Hang
• 0
1
vote
3
replies
150
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
updated 14 hours ago by
jared.andrews07
★ 16k • written 18 hours ago by
yvonneh
▴ 10
1
vote
2
replies
123
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
15 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
110
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
16 hours ago by
dtnondorf
• 0
0
votes
1
reply
133
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
0
votes
1
reply
122
views
RNA-seq data for deep learning classification
rna-seq
updated 17 hours ago by
dsull
★ 5.9k • written 19 hours ago by
Yuju
• 0
2
votes
6
replies
251
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
459
views
Loss of 'var' using concatenation of AnnData objects
Scanpy
AnnData
updated 19 hours ago by
Hugo
• 0 • written 4 months ago by
Rachel
• 0
0
votes
1
reply
98
views
Provean help
variant
Provean
updated 16 hours ago by
Mensur Dlakic
★ 27k • written 19 hours ago by
Arun Sai Kumar
• 0
1
vote
1
reply
117
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL
GTEx
updated 19 hours ago by
bk11
★ 2.4k • written 1 day ago by
Jeol
▴ 20
1
vote
1
reply
123
views
Super ehancers
enhancers
updated 20 hours ago by
jared.andrews07
★ 16k • written 1 day ago by
Oburah
• 0
0
votes
3
replies
140
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
updated 1 hour ago by
i.sudbery
19k • written 21 hours ago by
Chen
• 0
5
votes
5
replies
211
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA
DADA2
metabarcoding
updated 21 hours ago by
atharvakarkare14
▴ 30 • written 1 day ago by
Begonia_pavonina
▴ 150
1
vote
7
replies
364
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
10 minutes ago by
eebloom
▴ 80
3
votes
3
replies
189
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression
RNA
NOISeq
DGE
updated 1 hour ago by
ATpoint
82k • written 23 hours ago by
alifafiq1
• 0
0
votes
0
replies
75
views
News:
Beyond beginner R: Advancing your coding skills - September 16-19
Advanced-Coding
Programming
R
updated 19 hours ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
195
views
Subsetting and merging back Seurat Object brings different results
Seurat
22 hours ago by
Bine
▴ 60
0
votes
0
replies
100
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
NGS
Genomics
Post-doc
R-loops
updated 19 hours ago by
Ram
43k • written 1 day ago by
4r-rtg
• 0
1
vote
1
reply
117
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
1
reply
114
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
9
votes
10
replies
434
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 19 hours ago by
Zamin Iqbal
▴ 20 • written 1 day ago by
nicole.kavanagh
• 0
1
vote
3
replies
181
views
Odd alignment question/finding
Alignment
updated 1 hour ago by
barslmn
★ 2.1k • written 1 day ago by
poordumbsillyidiot
• 0
0
votes
7
replies
487
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 10 hours ago by
LChart
3.9k • written 3 days ago by
kl
▴ 10
0
votes
1
reply
767
views
cnetplot category names are too long
clusterprofiler
RNA-Seq
enrichplot
cnetplot
updated 19 hours ago by
Ram
43k • written 2.7 years ago by
carov
• 0
1
vote
5
replies
281
views
Introduce SNPs on FASTA
simulation
snps
haplotypes
pharmacogenetics
2 hours ago by
Riccardo
▴ 10
0
votes
5
replies
268
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 3 hours ago by
Mohamed Abderrahmane
▴ 20 • written 4 days ago by
matteo.levorato
• 0
5
votes
4
replies
343
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
21 hours ago by
Estevão
• 0
1
vote
4
replies
246
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
16 minutes ago by
eebloom
▴ 80
1
vote
2
replies
247
views
read length in structural variant calling
nanopore
SV
QC
ONT
variant
11 minutes ago by
eebloom
▴ 80
1
vote
4
replies
1.0k
views
Filtering qscore on dorado
dorado
filtering
QC
nanopore
Guppy
21 hours ago by
eebloom
▴ 80
29
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split
fastq
updated 17 hours ago by
thomas.heigl.ibk
• 0 • written 12.8 years ago by
Bioscientist
★ 1.7k
0
votes
1
reply
534
views
HOMER on AWS
HOMER
updated 8 hours ago by
clairechung112
• 0 • written 2.2 years ago by
Bogdan
★ 1.4k
16
votes
12
replies
7.3k
views
10 follow
how to split multi-fasta file into single fasta file named by header
genome
perl
python3
bash
python
updated 2 hours ago by
rsieber
▴ 10 • written 3.1 years ago by
Kumar
▴ 120
1
vote
14
replies
2.3k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 14 hours ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
47 results • Page
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Recent Votes
Answer: Controlling for FDR in 450k methylation microarray data
Comment: Generating mpileup file using samtools
Comment: Generating mpileup file using samtools
Answer: Downsampling long-read BAM files
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
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Recent Replies
Comment: Generating mpileup file using samtools
by
Ruqaiya
• 0
I didn't use the same tool as in the paper...
Comment: read length in structural variant calling
by
eebloom
▴ 80
Yes good idea. I guess the quality of the SV calls and as a proxy for quality the length and distribution of variants called might be infor…
Comment: Generating mpileup file using samtools
by
Ruqaiya
• 0
I just realised I didn't align my reads with the tools they used and used bowtie2 instead. The tool isn't available on conda and I can't fi…
Comment: Downsampling long-read BAM files
by
eebloom
▴ 80
This is not what I needed for this particular use case, as capping the coverage would lose the information on regions of copy number amplif…
Comment: Do I need to go back and filter my long-reads?
by
eebloom
▴ 80
Apologies, I deleted the question as I wasn't sure it would be helpful to others and it didn't seem to have a clear answer, not to snub the…
Comment: Do I need to go back and filter my long-reads?
by
eebloom
▴ 80
Thanks, I think it would be a good idea to track the results downstream to look for batch effects. I think I will filter the reads ultimate…
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
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