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80 results • Page
2 of 2
Sort: Votes
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Votes
Replies
0
votes
0
replies
99
views
barcode of TCR-sequencing
barcode
1 day ago by
yueli7
▴ 250
0
votes
0
replies
98
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 1 day ago by
Ram
43k • written 1 day ago by
Alexandros
• 0
0
votes
1
reply
134
views
unable to get feature count results
featureCounts
updated 1 day ago by
Ram
43k • written 1 day ago by
Ravita
• 0
0
votes
3
replies
239
views
KEGG Pathways
r
RNA-seq
updated 1 day ago by
Ram
43k • written 1 day ago by
Sudip
• 0
0
votes
0
replies
91
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
283
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 21 hours ago by
Ram
43k • written 1 day ago by
Dr Huma Naz
• 0
0
votes
1
reply
143
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
updated 21 hours ago by
Ram
43k • written 1 day ago by
rianna.collins
• 0
0
votes
1
reply
123
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 15 hours ago by
i.sudbery
19k • written 1 day ago by
Edmond
• 0
0
votes
0
replies
49
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
10 hours ago by
VITALA
• 0
0
votes
5
replies
286
views
Telescope issue
Telescope
RNA-seq
updated 9 hours ago by
GenoMax
141k • written 1 day ago by
eleven11
• 0
0
votes
1
reply
75
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 8 hours ago by
Ram
43k • written 10 hours ago by
ernestine.kubi
• 0
0
votes
1
reply
138
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
updated 7 hours ago by
Adam
▴ 30 • written 1 day ago by
Ahiad Chen Zion
• 0
0
votes
0
replies
30
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
5 hours ago by
meck
• 0
0
votes
0
replies
48
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 3 hours ago by
Ram
43k • written 5 hours ago by
Oscar
▴ 10
0
votes
1
reply
54
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 56 minutes ago by
GenoMax
141k • written 4 hours ago by
mgranada3
▴ 30
0
votes
0
replies
151
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
6 days ago by
Aspire
▴ 330
0
votes
5
replies
353
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 6 days ago by
GenoMax
141k • written 7 days ago by
Bertalan_Takacs
▴ 90
0
votes
1
reply
489
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 6 days ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
0
votes
0
replies
153
views
how to read graph_test output of monocle 3
monocle3
6 days ago by
synat.keam
▴ 100
0
votes
0
replies
156
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
6 days ago by
Emily
▴ 10
0
votes
0
replies
169
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
6 days ago by
avocado123
• 0
0
votes
1
reply
218
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 6 days ago by
ATpoint
82k • written 6 days ago by
AaronJaime
• 0
0
votes
2
replies
260
views
Annovar using R package
Annovar
gnomAD
R
6 days ago by
DKA
▴ 40
0
votes
0
replies
163
views
Designing single-stable RNA molecules
structure
RNA
6 days ago by
Edna
• 0
0
votes
0
replies
173
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
6 days ago by
simplitia
▴ 130
0
votes
11
replies
550
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
6 days ago by
atowns21
• 0
0
votes
0
replies
153
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
5 days ago by
turcoa1
• 0
0
votes
0
replies
200
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
5 days ago by
HarperReed
• 0
0
votes
0
replies
170
views
RNA-seq: full length gene
RNA-seq
updated 5 days ago by
Ram
43k • written 5 days ago by
Nargis
• 0
0
votes
3
replies
295
views
Highest variable features in single cell data
single-cell
updated 5 days ago by
bk11
★ 2.4k • written 6 days ago by
Kazo
▴ 10
80 results • Page
2 of 2
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Recent Replies
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?
Answer: How to find overlap of clusters in two seurat porject
by
Adam
▴ 30
I think your best bet would be to use annotation mapping. You can use the features of your clusters in group 1 and apply them to group 2 to…
Answer: DESeq2 processing problems
by
Adam
▴ 30
> when I put in the dataset, I am not able to run it for DEG analysis because system asks me to remove the first column which is of gene na…
Comment: Bacterial plasmid analysis
by
nicole.kavanagh
• 0
Thank you so much for your quick response, I have been searching scientific papers for about a week but have failed to come up with a reaso…
Comment: Bacterial plasmid analysis
by
GenoMax
141k
> however I'm not sure this would be appropriate in my case as the plasmid sequences are obviously much more diverse and vary in size Can…
Answer: cnetplot category names are too long
by
bkleiboeker
▴ 370
I'm sure someone could find a more elegant solution using `stringr::str_wrap`, but for a one-time solution I did this: # my results of…
Comment: Telescope issue
by
GenoMax
141k
You could edit the SAM file but I wonder if this problem is present in your original fastq data file so if not inconvenient do the alignmen…
Comment: Mutect2 for mitochondria variant discovery
by
GenoMax
141k
> I keep getting error. Without providing information about the actual error no one can help. Please edit the post and add this informati…
Comment: Telescope issue
by
eleven11
• 0
Thank you! how would I correct that?
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