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90 results • Page
2 of 2
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Votes
Replies
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 5 days ago by
Emanoelle
• 0 • written 5.7 years ago by
Elizabeth
▴ 30
0
votes
0
replies
102
views
Pathway analysis of Bacteria from denovo genome assembly
KEGG-KASS
WGS
Pathway
denovo
updated 5 days ago by
Ram
43k • written 5 days ago by
mathavanbioinfo
▴ 90
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 5 days ago by
chloek88
• 0 • written 5.5 years ago by
Philipp Bayer
8.5k
4
votes
6
replies
396
views
RNA seq analysis
DESeq
RNA-seq
updated 17 hours ago by
Matthias Zepper
4.6k • written 5 days ago by
prifa
▴ 10
0
votes
0
replies
142
views
Chance for trained without experience
bio
updated 5 days ago by
ATpoint
82k • written 5 days ago by
shehab
• 0
0
votes
0
replies
119
views
Xenium multi sample data
batch
annotation
cell
Xenium
effect
5 days ago by
Omics data mining
▴ 260
0
votes
2
replies
178
views
Phasing a mixture of two individuals' DNA with long reads
long-reads
phasing
5 days ago by
njornet
▴ 20
0
votes
2
replies
205
views
Exploring Diet Effects in Single-Cell RNA Sequencing
batch_effect
scRNA
seurat
integration
updated 5 days ago by
Adam
▴ 30 • written 5 days ago by
Darya
• 0
0
votes
5
replies
253
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 5 days ago by
Joe
21k • written 5 days ago by
Lemonhope
• 0
0
votes
0
replies
174
views
Why does my Hi-C contact map show large regions making little to no contact?
BWA-MEM2
Hi-C
PretextMap
4 days ago by
Winter
• 0
0
votes
0
replies
102
views
meffil.snp.concordance
meffil
methylation
snp_concordance
6 days ago by
kyj222637
• 0
0
votes
1
reply
150
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
updated 5 days ago by
Bastien Hervé
5.3k • written 6 days ago by
sooni
▴ 20
1
vote
3
replies
240
views
STAR aligner error
RNA-seq
STAR
slurm
updated 5 days ago by
Ram
43k • written 6 days ago by
M.
▴ 30
0
votes
0
replies
97
views
monocle 3-- Could not get node in small cluster
monocle3
6 days ago by
synat.keam
▴ 100
0
votes
2
replies
202
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
5 days ago by
Nicholas
• 0
0
votes
1
reply
250
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 6 days ago by
GenoMax
142k • written 6 days ago by
Sony
▴ 10
5
votes
5
replies
291
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
6 days ago by
Chris
▴ 280
0
votes
2
replies
214
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 5 days ago by
swbarnes2
14k • written 6 days ago by
ahmad.sajad4541
• 0
1
vote
9
replies
358
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 3 days ago by
i.sudbery
19k • written 6 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
167
views
student
epitranscriptomics
updated 6 days ago by
ATpoint
82k • written 6 days ago by
useriwa
• 0
0
votes
0
replies
113
views
Imputation of missing genotypes
panel
beagle
imputation
6 days ago by
analyst
▴ 50
0
votes
3
replies
177
views
trying to count a pattern in my fastq file using bbduk
java
bbduk
bbmap
fastq
updated 6 days ago by
GenoMax
142k • written 6 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
4
replies
280
views
Correlation Analysis
statistics
methylation
NGS
expression
2 days ago by
Researcher
▴ 30
1
vote
2
replies
180
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
6 days ago by
robert.flynn.21
• 0
0
votes
0
replies
105
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
4 days ago by
Javier
• 0
1
vote
7
replies
503
views
Question regarding WGCNA
WGCNA
Network-construction
4 days ago by
deepak
• 0
0
votes
1
reply
291
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 6 days ago by
andres.firrincieli
3.6k • written 7 days ago by
Antonio
• 0
2
votes
3
replies
316
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 4 days ago by
bk11
★ 2.4k • written 9 days ago by
Yoosef
▴ 60
0
votes
2
replies
259
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 3 days ago by
GenoMax
142k • written 10 days ago by
Ximena
• 0
0
votes
2
replies
287
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 1 day ago by
Zhenyu Zhang
★ 1.2k • written 10 days ago by
yahn
• 0
0
votes
2
replies
243
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
6 days ago by
Ahiad Chen Zion
• 0
3
votes
3
replies
248
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 9 hours ago by
Ram
43k • written 14 days ago by
Adyasha
• 0
0
votes
0
replies
110
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass-spectrometry
Proteins
updated 9 hours ago by
Ram
43k • written 14 days ago by
atharvakarkare14
▴ 30
0
votes
0
replies
175
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
deeptools
correlation
3 hours ago by
Emily
▴ 20
0
votes
4
replies
401
views
Highest variable features in single cell data
single-cell
6 days ago by
carolofharvest
▴ 40
1
vote
4
replies
400
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 3 days ago by
GenoMax
142k • written 26 days ago by
aniigodwinn
• 0
1
vote
0
replies
175
views
phasing tumor long-reads
nanopore
ONT
haplotag
phasing
tumor
4 days ago by
eebloom
▴ 80
0
votes
2
replies
260
views
Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences
ANNOVAR
6 days ago by
sainavyav22
• 0
1
vote
4
replies
486
views
cellranger error message
multiplexing
cellranger
updated 3 days ago by
Max
• 0 • written 3 months ago by
Alivia
▴ 10
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 8 hours ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 0
90 results • Page
2 of 2
Recent Votes
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
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Comment: What does the 'E%' represent in BUSCO results?
Answer: What does the 'E%' represent in BUSCO results?
Answer: Combine Two Affymetrix Datasets With Same Platform
Comment: Kraken2 database
Comment: How does gene length effect the number of reads mapped
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Recent Replies
Comment: Is it necessary to do genotype quality filteration after snp calling with GATK
by
Pierre Lindenbaum
161k
see VQSR https://gatk.broadinstitute.org/hc/en-us/articles/360035531612-Variant-Quality-Score-Recalibration-VQSR and https://gatk.broadinst…
Comment: Snakemake wrapper issue
by
Matvii Mykhailichenko
• 0
Hi, I kind of did and kind of didn't: I stopped trying to use snakemake( I remember that it's a lot of hustle to install pickard, maybe you…
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Hi, you can add the labels outside chart using `geom_label_repel` from `ggrepel` package. Check out this guide [https://r-charts.com/part…
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Wei-Chen Pan
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Hi, did you solve your problem ? I also encounter same issue but it's `wrapper:"v3.9.0/bio/picard/mergevcfs"`. In my log file, it said:…
Comment: What does the 'E%' represent in BUSCO results?
by
Philipp Bayer
8.5k
No worries! I found the commit with the maths too: https://gitlab.com/ezlab/busco/-/blame/master/src/busco/busco_tools/hmmer.py?page=2#L135…
Comment: What does the 'E%' represent in BUSCO results?
by
林明德
• 0
Thank you for your answer! It really helped me resolve a doubt!
Answer: What does the 'E%' represent in BUSCO results?
by
Philipp Bayer
8.5k
Ah your edit solved this. 50 BUSCOs contain internal stop codons, indicating they might be erroneous gene models, or the genes themselves a…
Answer: MGLTools does not work in windows 11
by
Ashfaq
• 0
In my case, I did not see iGPU. There is only one option, Intel UHD Graphics. What I need to do?
Comment: What does the 'E%' represent in BUSCO results?
by
Philipp Bayer
8.5k
funny enough i tried the same thing (i've used BUSCO heaps times but never saw the E:! even the manual lists 'C:89.0%[S:85.8%,D:3.2%],F:6.9…
Comment: What does the 'E%' represent in BUSCO results?
by
GenoMax
142k
According to ChatGPT: In BUSCO, the "E" category represents "End" or "Endof" gene fragments. These are orthologous groups for which the ge…
Comment: Help with IGV abbreviation
by
GeneC
• 0
Thank you for the link and details
Comment: Help with IGV abbreviation
by
GeneC
• 0
Thank you very much for helping with the details.
Comment: How does gene length effect the number of reads mapped
by
Chen
• 0
thank you :)
Answer: Filtering based on alternate allelic balance
by
Arton
• 0
I found the answer when using bcftools. Is there is a way to do this with FilterVcf? bcftools filter --include '(FMT/AD[0:1])/(FMT/A…
Comment: Help with IGV abbreviation
by
GenoMax
142k
Those are SAM format fields. Check section 1.4 here: https://samtools.github.io/hts-specs/SAMv1.pdf > 1:2114:12111:13792 That is part of …
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