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1,000 results • Page
1 of 20
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Views
Votes
Replies
0
votes
0
replies
24
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
30 minutes ago by
Vijith
▴ 30
0
votes
0
replies
29
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
2 hours ago by
Jeyong
• 0
0
votes
1
reply
83
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 8 hours ago by
Qroid
▴ 40 • written 9 hours ago by
Qi
• 0
0
votes
0
replies
45
views
Empty table plot using plotGseaTable()
FGSEA
9 hours ago by
Chris
▴ 260
1
vote
2
replies
112
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
10 hours ago by
Maverick
▴ 10
3
votes
8
replies
6.5k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 12 hours ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
101
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
12 hours ago by
dtnondorf
• 0
0
votes
1
reply
110
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
updated 4 hours ago by
Chris Dean
▴ 390 • written 13 hours ago by
sovrappensiero
▴ 90
2
votes
6
replies
234
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
6 hours ago by
Qroid
▴ 40
0
votes
1
reply
90
views
Provean help
variant
Provean
updated 12 hours ago by
Mensur Dlakic
★ 27k • written 15 hours ago by
Arun Sai Kumar
• 0
0
votes
0
replies
64
views
Use of annotation of integrated Seurat object in single sample
Seurat
20 hours ago by
Bine
▴ 60
0
votes
1
reply
188
views
Subsetting and merging back Seurat Object brings different results
Seurat
18 hours ago by
Bine
▴ 60
1
vote
1
reply
109
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 15 hours ago by
Ram
43k • written 22 hours ago by
marco.barr
▴ 90
0
votes
0
replies
63
views
edgeR contrasts for analysis of reciprocal hybrid crosses - averaging, pooling, and comparing groups
edgeR
22 hours ago by
Rhiannon
• 0
0
votes
1
reply
107
views
How to perform single cell multimodal integration using Seurat for Geo datasets
multimodal-analysis
single-cell
updated 12 hours ago by
Ram
43k • written 1 day ago by
nithya
• 0
0
votes
0
replies
72
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
1 day ago by
Vijith
▴ 30
0
votes
0
replies
71
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
1 day ago by
James
▴ 10
0
votes
1
reply
561
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 1 day ago by
mdav
• 0 • written 18 months ago by
Zoe
• 0
1
vote
2
replies
159
views
Odd alignment question/finding
Alignment
updated 23 hours ago by
ATpoint
82k • written 1 day ago by
poordumbsillyidiot
• 0
0
votes
1
reply
179
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 1 day ago by
GenoMax
142k • written 1 day ago by
mgranada3
▴ 30
0
votes
0
replies
76
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
1 day ago by
meck
• 0
0
votes
0
replies
106
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 1 day ago by
Ram
43k • written 1 day ago by
Oscar
▴ 10
0
votes
1
reply
124
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
93
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
1 day ago by
VITALA
• 0
1
vote
2
replies
228
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
1 day ago by
rianna.collins
• 0
0
votes
1
reply
165
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 1 day ago by
i.sudbery
19k • written 2 days ago by
Edmond
• 0
0
votes
0
replies
131
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
2 days ago by
O.rka
▴ 710
0
votes
1
reply
495
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 2 days ago by
Ram
43k • written 2 days ago by
Dr Huma Naz
• 0
0
votes
5
replies
335
views
Telescope issue
Telescope
RNA-seq
updated 1 day ago by
GenoMax
142k • written 2 days ago by
eleven11
• 0
1
vote
1
reply
216
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 2 days ago by
Ram
43k • written 2 days ago by
Jonathan Yoou
▴ 60
1
vote
2
replies
272
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
259
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 2 days ago by
GenoMax
142k • written 2 days ago by
jeffrey.maurer.informatics
• 0
0
votes
1
reply
168
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
0
votes
0
replies
122
views
barcode of TCR-sequencing
barcode
2 days ago by
yueli7
▴ 250
0
votes
0
replies
116
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
157
views
unable to get feature count results
featureCounts
updated 2 days ago by
Ram
43k • written 2 days ago by
Ravita
• 0
0
votes
3
replies
261
views
KEGG Pathways
r
RNA-seq
updated 2 days ago by
Ram
43k • written 2 days ago by
Sudip
• 0
0
votes
0
replies
124
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
2 days ago by
Bine
▴ 60
0
votes
0
replies
123
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
2 days ago by
8armed
• 0
1
vote
2
replies
213
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 2 days ago by
Ram
43k • written 2 days ago by
Ravita
• 0
0
votes
0
replies
107
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
3 days ago by
Adyasha
• 0
0
votes
0
replies
110
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
3 days ago by
fanglujing
▴ 60
0
votes
0
replies
125
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
3 days ago by
Jacob
• 0
0
votes
1
reply
177
views
Differential Accessibility
DiffBind
updated 3 days ago by
Ram
43k • written 3 days ago by
Shloka
• 0
0
votes
3
replies
270
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 2 days ago by
GenoMax
142k • written 3 days ago by
kim
• 0
3
votes
7
replies
322
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
3 days ago by
salias
• 0
0
votes
0
replies
121
views
Using limma in methylation EM-seq?
EM-seq
methylation
3 days ago by
Lluís R.
★ 1.2k
0
votes
0
replies
121
views
Synteny analysis
bacterial
synteny
genome
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Namil
• 0
0
votes
4
replies
240
views
Genbank File Format
gbkformat
2 days ago by
alenew.am
• 0
0
votes
0
replies
221
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
3 days ago by
SSSJec
• 0
1,000 results • Page
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Recent Votes
Answer: Two references 1. genome 2. plasmid for bowtie2
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Answer: Where Can I Download Some Bam Files?
Download SAM/BAM files from SRA takes ages!!!
Comment: Bedtools merge minimum overlap?
Convert sra to bam file error handling
Answer: Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
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Recent Replies
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Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
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Was the spike-in a commercial product, e.g., from Zymo? Can you provide more information about what cells or DNA was spiked into your samp…
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Comment: How to access TCGA samples that were treated with a specific drug?
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Thanks. Really appreciate your help with this. This site is such a great resource. The methods aren't totally clear on how they're gettin…
Comment: How to access TCGA samples that were treated with a specific drug?
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Are you thinking about a specific scenario? If so, can you provide more info? I think the basic answer is that, yes, your choice of group C…
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Bedtools [intersect][1] allows you to specify the fraction of overlap between two BED (or BAM) files using the F/f/r flags. You could split…
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