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1,068 results • Page
1 of 22
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0
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replies
6
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
updated just now by
Ram
43k • written 4 minutes ago by
dtnondorf
• 0
0
votes
0
replies
14
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
36 minutes ago by
sovrappensiero
▴ 90
0
votes
1
reply
46
views
RNA-seq data for deep learning classification
rna-seq
updated 39 minutes ago by
dsull
★ 5.9k • written 2 hours ago by
Yuju
• 0
1
vote
1
reply
32
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
updated 55 minutes ago by
Ram
43k • written 1 hour ago by
Qroid
▴ 40
1
vote
2
replies
31
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
10 minutes ago by
yvonneh
▴ 10
0
votes
0
replies
15
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
1 hour ago by
Hang
• 0
0
votes
1
reply
411
views
Loss of 'var' using concatenation of AnnData objects
Scanpy
AnnData
updated 2 hours ago by
Hugo
• 0 • written 4 months ago by
Rachel
• 0
0
votes
0
replies
24
views
Provean help
variant
Provean
updated 55 minutes ago by
Ram
43k • written 2 hours ago by
Arun Sai Kumar
• 0
0
votes
1
reply
72
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL
GTEx
updated 2 hours ago by
bk11
★ 2.4k • written 12 hours ago by
Jeol
▴ 20
1
vote
1
reply
83
views
Super ehancers
enhancers
updated 3 hours ago by
jared.andrews07
★ 16k • written 8 hours ago by
Oburah
• 0
0
votes
4
replies
110
views
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 3 hours ago by
jared.andrews07
★ 16k • written 3 hours ago by
JH
• 0
0
votes
2
replies
61
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
46 minutes ago by
Chen
• 0
5
votes
5
replies
160
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA
DADA2
metabarcoding
updated 4 hours ago by
atharvakarkare14
▴ 30 • written 7 hours ago by
Begonia_pavonina
▴ 150
0
votes
6
replies
325
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
updated 3 hours ago by
GenoMax
142k • written 22 days ago by
eesiribloom
▴ 80
1
vote
1
reply
88
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 2 hours ago by
Ram
43k • written 5 hours ago by
alifafiq1
• 0
0
votes
0
replies
43
views
Use of annotation of integrated Seurat object in single sample
Seurat
7 hours ago by
Bine
▴ 60
0
votes
0
replies
46
views
News:
Beyond beginner R: Advancing your coding skills - September 16-19
Advanced-Coding
Programming
R
updated 2 hours ago by
Ram
43k • written 8 hours ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
167
views
Subsetting and merging back Seurat Object brings different results
Seurat
5 hours ago by
Bine
▴ 60
0
votes
0
replies
63
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
NGS
Genomics
Post-doc
R-loops
updated 2 hours ago by
Ram
43k • written 9 hours ago by
4r-rtg
• 0
1
vote
1
reply
87
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 2 hours ago by
Ram
43k • written 9 hours ago by
marco.barr
▴ 90
0
votes
0
replies
43
views
edgeR contrasts for analysis of reciprocal hybrid crosses - averaging, pooling, and comparing groups
edgeR
9 hours ago by
Rhiannon
• 0
0
votes
1
reply
84
views
How to perform single cell multimodal integration using Seurat for Geo datasets
cell
analysis
multimodal
single
updated 10 hours ago by
ATpoint
82k • written 11 hours ago by
nithya
• 0
0
votes
0
replies
52
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
12 hours ago by
Vijith
▴ 30
9
votes
10
replies
371
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 2 hours ago by
Zamin Iqbal
▴ 20 • written 1 day ago by
nicole.kavanagh
• 0
0
votes
1
reply
229
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
updated 13 hours ago by
Scooter
▴ 280 • written 7 days ago by
avocado123
• 0
0
votes
0
replies
52
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
14 hours ago by
James
▴ 10
0
votes
1
reply
544
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 16 hours ago by
mdav
• 0 • written 18 months ago by
Zoe
• 0
1
vote
2
replies
136
views
Odd alignment question/finding
Alignment
updated 10 hours ago by
ATpoint
82k • written 16 hours ago by
poordumbsillyidiot
• 0
0
votes
1
reply
158
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 17 hours ago by
GenoMax
142k • written 21 hours ago by
mgranada3
▴ 30
0
votes
0
replies
60
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
22 hours ago by
meck
• 0
0
votes
0
replies
86
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 20 hours ago by
Ram
43k • written 22 hours ago by
Oscar
▴ 10
0
votes
6
replies
413
views
Post-imputation plot
michigan-imputation-server
quality-control
20 hours ago by
kl
▴ 10
0
votes
1
reply
173
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
250
views
DESeq2 processing problems
deseq2
R
updated 1 day ago by
ATpoint
82k • written 1 day ago by
jagdish7921
• 0
0
votes
1
reply
743
views
cnetplot category names are too long
clusterprofiler
RNA-Seq
enrichplot
cnetplot
updated 2 hours ago by
Ram
43k • written 2.7 years ago by
carov
• 0
0
votes
1
reply
104
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
74
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
1 day ago by
VITALA
• 0
1
vote
2
replies
211
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
12 hours ago by
rianna.collins
• 0
0
votes
1
reply
146
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
112
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
409
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
235
views
p-value in CIBERSORT
CIBERSORT
p-value
1 day ago by
michelafrancesconi9
▴ 20
0
votes
5
replies
316
views
Telescope issue
Telescope
RNA-seq
updated 1 day ago by
GenoMax
142k • written 1 day ago by
eleven11
• 0
5
votes
6
replies
472
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 2 days ago by
me
▴ 760 • written 3 days ago by
Mariana
▴ 40
1
vote
1
reply
208
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 2 days ago by
Jonathan Yoou
▴ 60
1
vote
2
replies
263
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
251
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 1 day ago by
GenoMax
142k • written 2 days ago by
jeffrey.maurer.informatics
• 0
0
votes
2
replies
205
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
150
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
165
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
1,068 results • Page
1 of 22
Recent Votes
Comment: How to access TCGA samples that were treated with a specific drug?
C: GATK genomicsDBimport intervals for WGS
Comment: DiffBind: no peaks in DBA
Comment: When should I NOT apply batch correction for my single-cell RNAseq data?
Comment: Bacterial plasmid analysis
Answer: Problem with data downloaded from Short Reads Archive (SRA)
Answer: Super ehancers
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curious
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Recent Replies
Comment: DiffBind: no peaks in DBA
by
yvonneh
▴ 10
Ok fixed!
Comment: Extract gRNA sequence using cutadapt
by
GenoMax
142k
Can you try lowering the `k` to `k=9`? You don't have any duplicate sequences in your library file? That may be one reason why bbduk is r…
Comment: Extract gRNA sequence using cutadapt
by
gernophil
▴ 80
This topic is almost 5 years old, but I am facing the same (or at least a very similar) issue. I have ngs files from a CRISPR screen that …
Answer: RNA-seq data for deep learning classification
by
dsull
★ 5.9k
Honestly speaking, if it's deep learning, it probably doesn't matter that much if you use something like TPMs (probably not raw counts, unl…
Comment: How does gene length effect the number of reads mapped
by
Chen
• 0
Thanks for the detailed answer and I really appreciate it! I still have one question about why the number of reads can be influenced by the…
Comment: Split Fastq Files Into Chunks Of 1M Reads
by
thomas.heigl.ibk
• 0
i tried it. it splits, however, when i compare the first 8 lines of the second split file with the according lines from the original file, …
Comment: DiffBind: no peaks in DBA
by
Ram
43k
> I've also included the txt version of my .csv file No, you added a screenshot of plain text content, which is counterproductive. You can…
Comment: How to access TCGA samples that were treated with a specific drug?
by
GenoMax
142k
At the GDC portal you have to turn the "therapeutic agents" toggle under "Clinical Data Analysis" on. ![drug][1] For Breast cancer you c…
Answer: Loss of 'var' using concatenation of AnnData objects
by
Hugo
• 0
Similar question has been asked and answered on [scverse discourse](https://discourse.scverse.org/t/loosing-anndata-var-layer-when-using-sc…
Comment: Bacterial plasmid analysis
by
Zamin Iqbal
▴ 20
Hi Nicole. 1. The clustering will be quite different between pling and the rep types (because plasmids with one rep type can still be ve…
Comment: Do I need to go back and filter my long-reads?
by
Ram
43k
Do not delete posts that have received feedback. Engage with the user providing you feedback.
Answer: Download eQTL data of one specific gene for all tissues from GTEx
by
bk11
★ 2.4k
Please kindly check your result here. You can click `csv` and download the date in this [link][1]. **OR** If you prefer to use R, there i…
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…
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