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25 results • Page
1 of 1
Sort: Votes
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Votes
Replies
2
votes
2
replies
220
views
p-value in CIBERSORT
CIBERSORT
p-value
23 hours ago by
michelafrancesconi9
▴ 20
1
vote
2
replies
250
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
21 hours ago by
Nafi
• 0
1
vote
6
replies
204
views
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 10 minutes ago by
shenwei356
8.4k • written 16 hours ago by
nicole.kavanagh
• 0
1
vote
3
replies
233
views
DESeq2 processing problems
deseq2
R
updated 15 hours ago by
ATpoint
82k • written 1 day ago by
jagdish7921
• 0
1
vote
2
replies
186
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
3 hours ago by
rianna.collins
• 0
1
vote
2
replies
75
views
Odd alignment question/finding
Alignment
updated 1 hour ago by
ATpoint
82k • written 7 hours ago by
poordumbsillyidiot
• 0
1
vote
0
replies
7
views
Discrepancy in read counts from fastq
reads
downsampling
fastq
count
13 minutes ago by
marco.barr
▴ 90
0
votes
1
reply
90
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 15 hours ago by
Ram
43k • written 17 hours ago by
ernestine.kubi
• 0
0
votes
1
reply
154
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
updated 15 hours ago by
Adam
▴ 30 • written 1 day ago by
Ahiad Chen Zion
• 0
0
votes
1
reply
132
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 22 hours ago by
i.sudbery
19k • written 1 day ago by
Edmond
• 0
0
votes
0
replies
46
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
12 hours ago by
meck
• 0
0
votes
0
replies
69
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 11 hours ago by
Ram
43k • written 12 hours ago by
Oscar
▴ 10
0
votes
6
replies
390
views
Post-imputation plot
michigan-imputation-server
quality-control
10 hours ago by
kl
▴ 10
0
votes
1
reply
120
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 8 hours ago by
GenoMax
141k • written 11 hours ago by
mgranada3
▴ 30
0
votes
1
reply
521
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 7 hours ago by
mdav
• 0 • written 18 months ago by
Zoe
• 0
0
votes
0
replies
29
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
5 hours ago by
James
▴ 10
0
votes
1
reply
204
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
updated 4 hours ago by
Scooter
▴ 280 • written 6 days ago by
avocado123
• 0
0
votes
0
replies
8
views
edgeR contrasts for analysis of reciprocal hybrid crosses - averaging, pooling, and comparing groups
edgeR
30 minutes ago by
Rhiannon
• 0
0
votes
0
replies
25
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
3 hours ago by
Vijith
▴ 30
0
votes
0
replies
26
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL
GTEx
3 hours ago by
Jeol
▴ 20
0
votes
1
reply
38
views
How to perform single cell multimodal integration using Seurat for Geo datasets
cell
analysis
multimodal
single
updated 1 hour ago by
ATpoint
82k • written 2 hours ago by
nithya
• 0
0
votes
0
replies
60
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
17 hours ago by
VITALA
• 0
0
votes
5
replies
302
views
Telescope issue
Telescope
RNA-seq
updated 16 hours ago by
GenoMax
141k • written 1 day ago by
eleven11
• 0
0
votes
1
reply
729
views
cnetplot category names are too long
RNASeq
clusterprofiler
cnetplot
enrichplot
updated 16 hours ago by
bkleiboeker
▴ 370 • written 2.7 years ago by
carov
• 0
0
votes
1
reply
162
views
How to find overlap of clusters in two seurat porject
clustering
seurat
updated 15 hours ago by
Adam
▴ 30 • written 1 day ago by
J
• 0
25 results • Page
1 of 1
Recent Votes
Discrepancy in read counts from fastq
R: Unable to use analyzeFeatures because argument is not a vector
Comment: Odd alignment question/finding
Comment: POSSUM not working due to incompatible pssm file
Comment: Can't install AnnotationHub
C: TOPGO- how to do GO enrichment using a custom go database?
Answer: NGS forensics: how to know if data is fabricated
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Jeol
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nicole.kavanagh
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Recent Replies
Comment: Bacterial plasmid analysis
by
shenwei356
8.4k
My colleague has an unpublished tool for plasmid analysis (clustering), and it has really good results. You might have a try. https://githu…
Comment: Odd alignment question/finding
by
ATpoint
82k
bwa mem is not fully deterministic, see from the developer: https://www.biostars.org/p/238628/#238817
Comment: How to perform single cell multimodal integration using Seurat for Geo datasets
by
ATpoint
82k
It's funny that you ask because the paper that these data were used for is called `Integrated analysis of multimodal single-cell data` from…
Comment: Odd alignment question/finding
by
liorglic
★ 1.4k
I can't come up with an explanation, but two things you can try for debugging are: 1) look at the fastp stats - do they add up and make sen…
Answer: Bacterial plasmid analysis
by
Mensur Dlakic
★ 27k
If you put all your sequences in separate files but in the same directory, this program will build a cladogram based on average nucleotide …
Comment: POSSUM not working due to incompatible pssm file
by
rianna.collins
• 0
Thank you so much. I'm new to this and didn't realise there was a code option.
Answer: Is there a way to increase the automatic label text size in Cytoscape?
by
Scooter
▴ 280
Greetings, Are you saying that you can't use the size setting in the style tab? That should certainly work, as should the label size se…
Answer: Basic stats in hierfstat
by
mdav
• 0
Hi Zoe, did you find an answer for this? I am also getting the same error.
Comment: GATK won't produce figures while analyzing covariates to generate 'recal_plots.p
by
GenoMax
141k
Your cluster may be missing libraries etc to create the PDF plots (this looks like a cluster job submission) on your cluster. Did you check…
Comment: Post-imputation plot
by
kl
▴ 10
Ok yes I think my thought was that given these errors, I could remove the mismatches and flip the alleles which seem to need flipping based…
Comment: Bacterial plasmid analysis
by
nicole.kavanagh
• 0
I think I will perhaps use their predominant PlasmidFinder type to group plasmids together and create separate core phylogenies for each as…
Comment: Bacterial plasmid analysis
by
GenoMax
141k
Can you classify the plasmids based on function (resistance genes they are carrying or some other criteria). Sizes above are indicating a w…
Comment: DESeq2 processing problems
by
ATpoint
82k
Initially posted here https://support.bioconductor.org/p/9158036/ where I suggested to put code and data and noted that GEOquery returns ar…
Answer: Post-imputation plot
by
LChart
3.9k
I agree that some need to be flipped (A/T and C/G where your panel frequency is 1 - ref panel frequency). There are other variants which yo…
Comment: RNA editing sites based on DNA seq and RNA seq
by
Adam
▴ 30
Are those 20% unaligned reads coming after hyper-editing detection?
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