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1,000 results • Page
1 of 20
Sort: Rank
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Views
Votes
Replies
0
votes
1
reply
16
views
Generating mpileup file using samtools
mpileup
samtools
updated 10 minutes ago by
Joe
21k • written 30 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 19 hours ago by
JH
• 0
0
votes
3
replies
117
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
146
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
50
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 13 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 13 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
124
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 19 hours ago by
GenoMax
142k • written 22 days ago by
eesiribloom
▴ 80
1
vote
2
replies
138
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
115
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
0
replies
68
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
111
views
How to perform single cell multimodal integration using Seurat for Geo datasets
multimodal-analysis
single-cell
updated 15 hours ago by
Ram
43k • written 1 day ago by
nithya
• 0
0
votes
0
replies
76
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
1 day ago by
Vijith
▴ 30
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
1
reply
253
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
updated 1 day ago by
Scooter
▴ 280 • written 7 days ago by
avocado123
• 0
0
votes
0
replies
77
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
1 day ago by
James
▴ 10
0
votes
1
reply
566
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 1 day ago by
mdav
• 0 • written 18 months ago by
Zoe
• 0
1
vote
2
replies
164
views
Odd alignment question/finding
Alignment
updated 1 day ago by
ATpoint
82k • written 1 day ago by
poordumbsillyidiot
• 0
0
votes
1
reply
183
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
80
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
1 day ago by
meck
• 0
0
votes
0
replies
110
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
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
197
views
How to find overlap of clusters in two seurat porject
clustering
seurat
updated 1 day ago by
Adam
▴ 30 • written 2 days ago by
J
• 0
1
vote
3
replies
279
views
DESeq2 processing problems
deseq2
R
updated 1 day ago by
ATpoint
82k • written 2 days ago by
jagdish7921
• 0
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
0
votes
1
reply
129
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
98
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
1 day ago by
VITALA
• 0
1
vote
2
replies
232
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
169
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 1 day 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
1,000 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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Recent Replies
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…
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…
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