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116,715 results • Page
1 of 2335
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0
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46
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Download eQTL data of one specific gene for all tissues from GTEx
eQTL
GTEx
updated just now by
bk11
★ 2.4k • written 9 hours ago by
Jeol
▴ 20
0
votes
1
reply
43
views
Super ehancers
enhancers
updated 4 minutes ago by
jared.andrews07
★ 16k • written 5 hours ago by
Oburah
• 0
0
votes
4
replies
49
views
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 14 minutes ago by
jared.andrews07
★ 16k • written 48 minutes ago by
JH
• 0
0
votes
1
reply
19
views
How goes gene length effect the number of reads mapped
CPM
RNA-seq
sequencing
updated 17 minutes ago by
i.sudbery
19k • written 1 hour ago by
Chen
• 0
4
votes
5
replies
112
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA
DADA2
metabarcoding
updated 56 minutes ago by
atharvakarkare14
▴ 20 • written 4 hours ago by
Begonia_pavonina
▴ 150
0
votes
6
replies
293
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
updated 52 minutes ago by
GenoMax
142k • written 22 days ago by
eesiribloom
▴ 80
1
vote
1
reply
56
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Expression
Gene
NOISeq
RNA
DGE
updated 2 hours ago by
ATpoint
82k • written 2 hours ago by
alifafiq1
• 0
0
votes
0
replies
32
views
Use of annotation of integrated Seurat object in single sample
Seurat
4 hours ago by
Bine
▴ 60
795
votes
167
replies
142k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
0
replies
36
views
News:
Beyond beginner R: Advancing your coding skills - September 16-19
AdvancedCoding
Programming
R
5 hours ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
158
views
Subsetting and merging back Seurat Object brings different results
Seurat
2 hours ago by
Bine
▴ 60
0
votes
0
replies
53
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
Biology
R-loops
Genomics
NGS
Post-doc
6 hours ago by
4r-rtg
• 0
1
vote
1
reply
72
views
Discrepancy in read counts from fastq
reads
downsampling
fastq
count
updated 3 hours ago by
GenoMax
142k • written 6 hours ago by
marco.barr
▴ 90
0
votes
0
replies
33
views
edgeR contrasts for analysis of reciprocal hybrid crosses - averaging, pooling, and comparing groups
edgeR
6 hours ago by
Rhiannon
• 0
0
votes
1
reply
73
views
How to perform single cell multimodal integration using Seurat for Geo datasets
cell
analysis
multimodal
single
updated 7 hours ago by
ATpoint
82k • written 8 hours ago by
nithya
• 0
0
votes
0
replies
45
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
9 hours ago by
Vijith
▴ 30
8
votes
9
replies
312
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
13 minutes ago by
nicole.kavanagh
• 0
0
votes
1
reply
225
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
updated 10 hours ago by
Scooter
▴ 280 • written 6 days ago by
avocado123
• 0
0
votes
0
replies
48
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
11 hours ago by
James
▴ 10
0
votes
1
reply
538
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 13 hours ago by
mdav
• 0 • written 18 months ago by
Zoe
• 0
1
vote
2
replies
125
views
Odd alignment question/finding
Alignment
updated 7 hours ago by
ATpoint
82k • written 13 hours ago by
poordumbsillyidiot
• 0
0
votes
1
reply
154
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 14 hours ago by
GenoMax
142k • written 18 hours ago by
mgranada3
▴ 30
0
votes
0
replies
56
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
18 hours ago by
meck
• 0
0
votes
0
replies
81
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 17 hours ago by
Ram
43k • written 19 hours ago by
Oscar
▴ 10
0
votes
6
replies
407
views
Post-imputation plot
michigan-imputation-server
quality-control
17 hours ago by
kl
▴ 10
0
votes
1
reply
168
views
How to find overlap of clusters in two seurat porject
clustering
seurat
updated 21 hours ago by
Adam
▴ 30 • written 1 day ago by
J
• 0
1
vote
3
replies
246
views
DESeq2 processing problems
deseq2
R
updated 21 hours ago by
ATpoint
82k • written 1 day ago by
jagdish7921
• 0
0
votes
1
reply
738
views
cnetplot category names are too long
RNASeq
clusterprofiler
cnetplot
enrichplot
updated 22 hours ago by
bkleiboeker
▴ 370 • written 2.7 years ago by
carov
• 0
0
votes
1
reply
99
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 21 hours ago by
Ram
43k • written 23 hours ago by
ernestine.kubi
• 0
0
votes
0
replies
70
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
23 hours ago by
VITALA
• 0
1
vote
2
replies
206
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
9 hours ago by
rianna.collins
• 0
0
votes
1
reply
141
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 1 day ago by
i.sudbery
19k • written 1 day ago by
Edmond
• 0
0
votes
0
replies
107
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
1 day ago by
O.rka
▴ 710
0
votes
1
reply
390
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 1 day ago by
Ram
43k • written 1 day ago by
Dr Huma Naz
• 0
2
votes
2
replies
230
views
p-value in CIBERSORT
CIBERSORT
p-value
1 day ago by
michelafrancesconi9
▴ 20
0
votes
5
replies
312
views
Telescope issue
Telescope
RNA-seq
updated 22 hours ago by
GenoMax
142k • written 1 day ago by
eleven11
• 0
5
votes
6
replies
463
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 1 day ago by
me
▴ 760 • written 3 days ago by
Mariana
▴ 40
1
vote
1
reply
203
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 1 day ago by
Ram
43k • written 1 day ago by
Jonathan Yoou
▴ 60
1
vote
2
replies
258
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
246
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 1 day ago by
GenoMax
142k • written 1 day ago by
jeffrey.maurer.informatics
• 0
0
votes
2
replies
198
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Dora
▴ 10
0
votes
0
replies
145
views
News:
Goodbye, Slow Code? How BioNumpy can Redefine Python’s Role in Bioinformatics!
BioNumPy
Python
NumPy
updated 2 days ago by
Ram
43k • written 2 days ago by
Chakri
• 0
0
votes
1
reply
162
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
updated 21 hours ago by
Adam
▴ 30 • written 2 days ago by
Ahiad Chen Zion
• 0
0
votes
4
replies
247
views
Introduce SNPs on FASTA
simulation
snps
haplotypes
pharmacogenetics
updated 2 days ago by
Michael
54k • written 2 days ago by
Riccardo
▴ 10
0
votes
0
replies
115
views
barcode of TCR-sequencing
barcode
2 days ago by
yueli7
▴ 250
0
votes
0
replies
118
views
News:
Online course: Meta-analysis in R - last 2 seats left
Meta-Analysis
Statistics
R
updated 2 days ago by
Ram
43k • written 2 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
113
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
155
views
unable to get feature count results
featureCounts
updated 1 day ago by
Ram
43k • written 2 days ago by
Ravita
• 0
0
votes
3
replies
259
views
KEGG Pathways
r
RNA-seq
updated 1 day ago by
Ram
43k • written 2 days ago by
Sudip
• 0
4
votes
6
replies
3.8k
views
Taking the difference of two VCFs (or removing singletons)
genome
sequencing
singleton
SNP
filter
updated 2 days ago by
Andres
▴ 20 • written 9.6 years ago by
hermathena
▴ 40
116,715 results • Page
1 of 2335
Recent Votes
Comment: Bacterial plasmid analysis
Answer: Why employ normalization methods, and how can they be utilized in DEG analysis?
Answer: Why employ normalization methods, and how can they be utilized in DEG analysis?
Answer: What analysis suitable to identify similarly expressed genes between two samples
Comment: Bacterial plasmid analysis
Comment: Problem with data downloaded from Short Reads Archive (SRA)
Comment: Problem with data downloaded from Short Reads Archive (SRA)
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Recent Replies
Comment: RNAseq one control two conditions, shared and exclusive genes
by
matteo.levorato
• 0
but why not a single matrix with the 3 different condition and then by lfcShrink function get the DEGs of each condition?
Answer: Super ehancers
by
jared.andrews07
★ 16k
Sure, you can run it on them. Stitching tends to happen less frequently since the ATAC peaks are generally less wide than H3K27ac, but it'l…
Answer: What purposes can TPM values be used for?
by
jared.andrews07
★ 16k
TPMs cannot be used for intersample comparisons, but they can be used for intrasample comparisons (e.g. comparing relative expression level…
Comment: Bacterial plasmid analysis
by
nicole.kavanagh
• 0
Thank you so much for the recommendation and the very clear explanation , it's much appreciated. I have already made core-gene phylogenies/…
Comment: What purposes can TPM values be used for?
by
Adam
▴ 30
Have you run FASTQC and checked the mapping efficiency of WT3? > would running DESeq using TPM values help solve my problem? No, DESeq sh…
Answer: How goes gene length effect the number of reads mapped
by
i.sudbery
19k
See my answer about the what hows and whens of RNA-seq normalisation here: https://www.biostars.org/p/9586553/#9586566
Comment: What purposes can TPM values be used for?
by
dsull
★ 5.9k
Since you have mutant vs wild-type, using DESeq2 is the right thing to do. Rather than showing a small table of numbers, you should make a …
Answer: What purposes can TPM values be used for?
by
i.sudbery
19k
See my post here for more details on RNA-seq normalisation: https://www.biostars.org/p/9586553/#9586566 In short, TPM normalises for ge…
Comment: Bacterial plasmid analysis
by
Zamin Iqbal
▴ 10
I vote for this, it's the best! (but also, I am Daria's PhD supervisor so I am biased). Preprint out soon(ish) [no pressure Daria!]
Comment: Downsampling long-read BAM files
by
GenoMax
142k
Is this what you used ultimately? Did this tool satisfy the "specific average depth" requirement? You could accept (green check mark) this…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
by
Estevão
• 0
Thank you. My budget is around 20 thousand dollars.
Answer: Problem with data downloaded from Short Reads Archive (SRA)
by
atharvakarkare14
▴ 20
Prefetch files using sratoolkit **prefetch** command and then use **fasterq-dump**. There you can see the number of reads. For validation, …
Answer: Downsampling long-read BAM files
by
eesiribloom
▴ 80
random downsampling of bam files is now possible using [rasusa][1] [v1.0.0][2] with the `aln` subcommand [1]: https://github.com/mbh…
Comment: Problem with data downloaded from Short Reads Archive (SRA)
by
GenoMax
142k
Use `vdb-validate` included in `sratoolkit` to check your `*.sra` files for integrity.
Comment: Problem with data downloaded from Short Reads Archive (SRA)
by
ATpoint
82k
This `fastq-dump --split-files *.sra` gives you fastq files. I am not sure how, with the given information, one might debug your problem. A…
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