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44 results • Page
1 of 1
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0
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1
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13
views
Generating mpileup file using samtools
mpileup
samtools
updated just now by
Joe
21k • written 20 minutes ago by
Ruqaiya
• 0
0
votes
5
replies
179
views
6 follow
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 1 hour ago by
b.contreras.moreira
▴ 180 • written 18 hours ago by
JH
• 0
0
votes
3
replies
114
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 1 hour ago by
ATpoint
82k • written 11 hours ago by
Qi
• 0
0
votes
0
replies
24
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
2 hours ago by
Amos Bairoch
▴ 120
0
votes
0
replies
41
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
2 hours ago by
Vijith
▴ 30
0
votes
0
replies
41
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
4 hours ago by
Jeyong
• 0
0
votes
2
replies
635
views
homer not configured properly
Homer
makeTagDirectory
updated 6 hours ago by
clairechung112
• 0 • written 23 months ago by
amahdi779
• 0
1
vote
3
replies
145
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 6 hours ago by
Alex Reynolds
35k • written 13 hours ago by
SJP
• 0
0
votes
0
replies
49
views
Empty table plot using plotGseaTable()
FGSEA
11 hours ago by
Chris
▴ 260
0
votes
1
reply
98
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 12 hours ago by
anovak
▴ 120 • written 16 hours ago by
Hang
• 0
1
vote
3
replies
147
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
updated 12 hours ago by
jared.andrews07
★ 16k • written 16 hours ago by
yvonneh
▴ 10
1
vote
2
replies
120
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
13 hours ago by
Maverick
▴ 10
3
votes
8
replies
6.5k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 14 hours ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
107
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
14 hours ago by
dtnondorf
• 0
0
votes
1
reply
123
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 6 hours ago by
Chris Dean
▴ 390 • written 15 hours ago by
sovrappensiero
▴ 90
0
votes
1
reply
115
views
RNA-seq data for deep learning classification
rna-seq
updated 15 hours ago by
dsull
★ 5.9k • written 17 hours ago by
Yuju
• 0
2
votes
6
replies
245
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
8 hours ago by
Qroid
▴ 40
0
votes
1
reply
456
views
Loss of 'var' using concatenation of AnnData objects
Scanpy
AnnData
updated 17 hours ago by
Hugo
• 0 • written 4 months ago by
Rachel
• 0
0
votes
1
reply
95
views
Provean help
variant
Provean
updated 14 hours ago by
Mensur Dlakic
★ 27k • written 17 hours ago by
Arun Sai Kumar
• 0
1
vote
1
reply
114
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL
GTEx
updated 17 hours ago by
bk11
★ 2.4k • written 1 day ago by
Jeol
▴ 20
1
vote
1
reply
120
views
Super ehancers
enhancers
updated 18 hours ago by
jared.andrews07
★ 16k • written 23 hours ago by
Oburah
• 0
0
votes
2
replies
128
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
15 hours ago by
Chen
• 0
5
votes
5
replies
208
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA
DADA2
metabarcoding
updated 19 hours ago by
atharvakarkare14
▴ 30 • written 22 hours ago by
Begonia_pavonina
▴ 150
0
votes
6
replies
356
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
updated 18 hours ago by
GenoMax
142k • written 22 days ago by
eesiribloom
▴ 80
1
vote
2
replies
137
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression
RNA
NOISeq
DGE
1 hour ago by
alifafiq1
• 0
0
votes
0
replies
70
views
Use of annotation of integrated Seurat object in single sample
Seurat
22 hours ago by
Bine
▴ 60
0
votes
0
replies
72
views
News:
Beyond beginner R: Advancing your coding skills - September 16-19
Advanced-Coding
Programming
R
updated 17 hours ago by
Ram
43k • written 23 hours ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
193
views
Subsetting and merging back Seurat Object brings different results
Seurat
20 hours ago by
Bine
▴ 60
0
votes
0
replies
96
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
NGS
Genomics
Post-doc
R-loops
updated 17 hours ago by
Ram
43k • written 1 day ago by
4r-rtg
• 0
1
vote
1
reply
114
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 17 hours ago by
Ram
43k • written 1 day ago by
marco.barr
▴ 90
0
votes
1
reply
111
views
How to perform single cell multimodal integration using Seurat for Geo datasets
multimodal-analysis
single-cell
updated 14 hours ago by
Ram
43k • written 1 day ago by
nithya
• 0
9
votes
10
replies
428
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 17 hours ago by
Zamin Iqbal
▴ 20 • written 1 day ago by
nicole.kavanagh
• 0
0
votes
7
replies
482
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 8 hours ago by
LChart
3.9k • written 3 days ago by
kl
▴ 10
0
votes
1
reply
766
views
cnetplot category names are too long
clusterprofiler
RNA-Seq
enrichplot
cnetplot
updated 17 hours ago by
Ram
43k • written 2.7 years ago by
carov
• 0
1
vote
5
replies
268
views
Introduce SNPs on FASTA
simulation
snps
haplotypes
pharmacogenetics
20 minutes ago by
Riccardo
▴ 10
0
votes
5
replies
249
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 1 hour ago by
Mohamed Abderrahmane
▴ 20 • written 3 days ago by
matteo.levorato
• 0
5
votes
4
replies
342
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
19 hours ago by
Estevão
• 0
1
vote
2
replies
235
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 17 hours ago by
Ram
43k • written 17 days ago by
eesiribloom
▴ 80
1
vote
0
replies
183
views
News:
Landscape Genomics course in Switzerland
LFMM
Landscape-Genomics
Sambada
R
Local-Adaptation
22 hours ago by
carlopecoraro2
★ 2.5k
1
vote
4
replies
1.0k
views
Filtering qscore on dorado
dorado
filtering
QC
nanopore
Guppy
19 hours ago by
eesiribloom
▴ 80
28
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split
fastq
updated 15 hours ago by
thomas.heigl.ibk
• 0 • written 12.8 years ago by
Bioscientist
★ 1.7k
0
votes
1
reply
526
views
HOMER on AWS
HOMER
updated 6 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 41 minutes 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 12 hours ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
44 results • Page
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Recent Votes
Comment: How to Calulate Allele Frequency from a VCF File?
Answer: Introduce SNPs on FASTA
Answer: how to split multi-fasta file into single fasta file named by header
How to Calulate Allele Frequency from a VCF File?
Answer: allele frequency in VCF
Answer: Two references 1. genome 2. plasmid for bowtie2
A: Iterating through paired-end reads in samtools / pysam
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Popular Question
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kuttibiotech2009
▴ 30
Popular Question
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analyst
▴ 30
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Shicheng Guo
★ 9.4k
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Recent Replies
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…
Comment: HOMER on AWS
by
clairechung112
• 0
Hi. I guess it is solved by now, but as I did not find the answer immediately online, here is the answer I posted on a relevant question: h…
Answer: homer not configured properly
by
clairechung112
• 0
A late reply, but I just solved exactly the same error upon a request in the team. Please see if it helps in case anyone meets the same err…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
Chris Dean
▴ 390
Was the spike-in a commercial product, e.g., from Zymo? Can you provide more information about what cells or DNA was spiked into your samp…
Comment: Bedtools merge minimum overlap?
by
Alex Reynolds
35k
Note that, in place of `sort-bed - | uniq -`, you can pass the `--unique` option to `sort-bed`. The input is not strictly a BED6 file, but…
Comment: Post-imputation plot
by
LChart
3.9k
Imputation takes what? A day or two of compute time? Just re-do it.
Comment: How to access TCGA samples that were treated with a specific drug?
by
Qroid
▴ 40
Thanks. Really appreciate your help with this. This site is such a great resource. The methods aren't totally clear on how they're gettin…
Comment: How to access TCGA samples that were treated with a specific drug?
by
GenoMax
142k
It is possible that these drugs may not have been directly used in TCGA. Authors could have looked for mutations known to be acted on by th…
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