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82 results • Page
2 of 2
Sort: Views
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Views
Votes
Replies
0
votes
0
replies
134
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
4 days ago by
tnminh89
▴ 10
0
votes
1
reply
134
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 23 hours ago by
i.sudbery
19k • written 1 day ago by
Edmond
• 0
0
votes
1
reply
124
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 2 days ago by
GenoMax
142k • written 3 days ago by
Winter
• 0
0
votes
1
reply
124
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 9 hours ago by
GenoMax
142k • written 12 hours ago by
mgranada3
▴ 30
0
votes
0
replies
122
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
2 days ago by
Jacob
• 0
0
votes
0
replies
117
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
2 days ago by
8armed
• 0
0
votes
0
replies
117
views
Synteny analysis
bacterial
synteny
genome
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Namil
• 0
0
votes
0
replies
115
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 2 days ago by
dariober
14k • written 4 days ago by
rene.j.erhardt
▴ 20
0
votes
0
replies
115
views
Using limma in methylation EM-seq?
EM-seq
methylation
2 days ago by
Lluís R.
★ 1.2k
0
votes
0
replies
113
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
2 days ago by
Bine
▴ 60
0
votes
0
replies
109
views
barcode of TCR-sequencing
barcode
1 day ago by
yueli7
▴ 250
0
votes
0
replies
107
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
0
replies
106
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
2 days ago by
fanglujing
▴ 60
0
votes
0
replies
103
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
2 days ago by
Adyasha
• 0
0
votes
0
replies
102
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
0
replies
98
views
LEfSe
LEfSe
2 days ago by
benkosta
• 0
0
votes
0
replies
96
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
3 days ago by
atharvakarkare14
▴ 20
0
votes
0
replies
92
views
vg call vs vg surject
vg
variation
graphs
updated 2 days ago by
GenoMax
142k • written 3 days ago by
aliraza3119
• 0
0
votes
1
reply
92
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 16 hours ago by
Ram
43k • written 18 hours ago by
ernestine.kubi
• 0
0
votes
0
replies
89
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
2 days ago by
David
• 0
1
vote
2
replies
85
views
Odd alignment question/finding
Alignment
updated 2 hours ago by
ATpoint
82k • written 8 hours ago by
poordumbsillyidiot
• 0
0
votes
0
replies
86
views
Differential accessibility using DiffBinf
diffbind
3 days ago by
Shloka
• 0
0
votes
0
replies
81
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
2 days ago by
Sara
▴ 30
0
votes
0
replies
72
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 12 hours ago by
Ram
43k • written 13 hours ago by
Oscar
▴ 10
0
votes
0
replies
62
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
18 hours ago by
VITALA
• 0
0
votes
1
reply
50
views
How to perform single cell multimodal integration using Seurat for Geo datasets
cell
analysis
multimodal
single
updated 2 hours ago by
ATpoint
82k • written 3 hours ago by
nithya
• 0
0
votes
0
replies
48
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
13 hours ago by
meck
• 0
0
votes
0
replies
36
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
6 hours ago by
James
▴ 10
0
votes
0
replies
32
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL
GTEx
4 hours ago by
Jeol
▴ 20
0
votes
0
replies
30
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
4 hours ago by
Vijith
▴ 30
1
vote
0
replies
15
views
Discrepancy in read counts from fastq
reads
downsampling
fastq
count
1 hour ago by
marco.barr
▴ 90
0
votes
0
replies
14
views
edgeR contrasts for analysis of reciprocal hybrid crosses - averaging, pooling, and comparing groups
edgeR
1 hour ago by
Rhiannon
• 0
82 results • Page
2 of 2
Recent Votes
Define enhancer regions
A: how can i download human ribosomal reference ?
Answer: Bacterial plasmid analysis
Answer: Bacterial plasmid analysis
Discrepancy in read counts from fastq
R: Unable to use analyzeFeatures because argument is not a vector
Comment: Odd alignment question/finding
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Apex92
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carlopecoraro2
★ 2.5k
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Recent Replies
Answer: Subsetting and merging back Seurat Object brings different results
by
Bine
▴ 60
Noone has an idea? Thank you!
Answer: Bacterial plasmid analysis
by
shenwei356
8.5k
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
142k
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
142k
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…
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