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94 results • Page
1 of 2
Sort: Votes
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Views
Votes
Replies
9
votes
15
replies
815
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
6 days ago by
analyst
▴ 10
6
votes
3
replies
247
views
How can I adjust Y-axis scale when making relative abundance box plot ?
statistics
box-plot
R
scale_adjustment
logarithm
updated 5 days ago by
Jeremy
▴ 860 • written 5 days ago by
ohtang7
▴ 40
4
votes
6
replies
416
views
bwa mem hangs after a few thousand reads
bwa-mem
alignment
bwa
calling
variant
5 days ago by
cee28
▴ 30
3
votes
6
replies
445
views
scRNA-seq: Consistent low number of cells and low fraction reads across the samples
scRNA-seq
cells
mRNA
expression
gene
updated 3 days ago by
jv
★ 1.2k • written 5 days ago by
newbee
▴ 40
3
votes
1
reply
197
views
KEGG DATABASE
DATABASE
KEGG
updated 2 days ago by
Mensur Dlakic
★ 25k • written 2 days ago by
Sijjil
• 0
3
votes
4
replies
319
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR
volcano
plotting
R
plot
updated 5 days ago by
Nitin Narwade
★ 1.5k • written 6 days ago by
RNAseqer
▴ 250
2
votes
9
replies
685
views
Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
STAR
Salmon
mapper
aligner
RNAseq
5 days ago by
ian.will
▴ 10
2
votes
2
replies
211
views
R script in docker
R
Visual_studio_code
Docker
4 days ago by
mrashad
▴ 70
2
votes
11
replies
683
views
Data preparation for a ML model
machine-learning
RNA-Seq
R
python
biomarkers
4 days ago by
sil_bioinfo
▴ 40
2
votes
1
reply
165
views
unicycler error : [Errno 13] Permission denied:
unicycler
updated 6 days ago by
barslmn
★ 2.0k • written 6 days ago by
jiyoung
▴ 20
2
votes
2
replies
817
views
Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when pivoting from wide to long format
rnaseq
pivot_longer
ggplot2
updated 6 days ago by
cmdcolin
★ 3.4k • written 6 days ago by
Dylan C-C
• 0
2
votes
1
reply
247
views
EnhancedVolcano underrepresenting DEGs
R
updated 6 days ago by
Kevin Blighe
86k • written 8 days ago by
jabbari.parnian
▴ 30
2
votes
5
replies
203
views
kallisto index build difference according to version
index
version
kallisto
updated 17 hours ago by
dsull
★ 5.1k • written 20 hours ago by
estilo
• 0
1
vote
1
reply
190
views
Match variants for allele frequency, LD score, and other features
snp
5 days ago by
Jautis
▴ 520
1
vote
3
replies
278
views
Identify clusters of populations based on gene expression
Seq
Single
cell
RNA
updated 6 days ago by
Nitin Narwade
★ 1.5k • written 6 days ago by
Bine
▴ 50
1
vote
2
replies
211
views
How can I amend the output of a DIAMOND python script?
Python
Diamond
COG_analysis
4 days ago by
eamaunders
• 0
1
vote
6
replies
523
views
frequency plot for peaks
chip-seq
chipseeker
updated 6 days ago by
Ankit
▴ 400 • written 21 days ago by
Mehwish
▴ 10
1
vote
4
replies
280
views
Bowtie mapping for single_end read
bowtie
6 days ago by
Rita
• 0
1
vote
1
reply
177
views
Harmony integration PC variance explained
scRNA
integration
harmony
updated 5 days ago by
CTLong
▴ 20 • written 7 days ago by
e.iich
• 0
1
vote
6
replies
366
views
Discrepancy in total number of bases in trimmed read1 and read2 files after BBDuk
bbduk
6 days ago by
CTLong
▴ 20
1
vote
2
replies
220
views
Problem in installing 'magick' R package
R
installation
package
magick
updated 5 days ago by
DBScan
▴ 210 • written 5 days ago by
applepie
• 0
1
vote
5
replies
1.5k
views
BLAST: overflow error
BLAST
updated 1 day ago by
GenoMax
136k • written 19 months ago by
antoinefelden
▴ 60
1
vote
3
replies
304
views
Bam files generated with STAR cause a segmentation fault core dump error when used with another tool
RNA-Seq
mapping
updated 20 hours ago by
GenoMax
136k • written 1 day ago by
bkffadia
• 0
0
votes
1
reply
162
views
How to check for incorporation of plasmid DNA into human genomic DNA (ChIP-seq)?
plasmid
chipseq
updated 4 days ago by
Nitin Narwade
★ 1.5k • written 5 days ago by
tss243
• 0
0
votes
2
replies
271
views
Cellcyclescoring did not work in Seurat V5
singlecell
updated 4 days ago by
fracarb8
★ 1.3k • written 5 days ago by
synat.keam
▴ 80
0
votes
1
reply
151
views
PAML Troubleshooting Help
PAML
codeml
updated 4 days ago by
dthorbur
▴ 890 • written 4 days ago by
sebabiokr
▴ 10
0
votes
3
replies
242
views
In what case there are RR reads but no LL reads when detect inversions using IGV?
IGV
inversion
updated 4 days ago by
Istvan Albert
99k • written 4 days ago by
Jingfang
• 0
0
votes
0
replies
124
views
How to do KEGG pathway analysis when I have a gene with multiple entrez IDs?
biomart
kegg
deseq2
4 days ago by
bioinfo
▴ 140
0
votes
0
replies
125
views
how to download the VCF/MAF files from cBioportal genie site
cBioportal
mutation
VCF
TMB
4 days ago by
luckyday1661
• 0
0
votes
1
reply
444
views
Loftee no splice site annotations
Loftee
VEP
updated 4 days ago by
AMARU
• 0 • written 21 months ago by
Filago
▴ 90
0
votes
0
replies
140
views
Extract upstream and downstream 50bp nontemplated sequences from a position
search
sequences
nontemplated
motif
4 days ago by
Ty
• 0
0
votes
1
reply
166
views
How to get multiple protein domain database domain name from id's
annotations
blast2go
domain
domains
proteins
updated 4 days ago by
GenoMax
136k • written 4 days ago by
Nicolas
• 0
0
votes
0
replies
138
views
Osmotic permeability of water transport in aquaporins
permeability
Osmotic
transport
Water
3 days ago by
Peerzada
• 0
0
votes
4
replies
1.2k
views
Adding functional annotation and meta-data of MAKER/BRAKER GFF
metadata
functional-annotation
BRAKER
MAKER
updated 3 days ago by
ben@f
• 0 • written 11 months ago by
javanokendo
▴ 20
0
votes
1
reply
185
views
Annotate Unplaced Scaffold with Chromosome Information
assembly
annotation
scaffold
Chromosome
updated 3 days ago by
cmdcolin
★ 3.4k • written 4 days ago by
Trevor
• 0
0
votes
0
replies
152
views
Significance of several BUSCO target IDs for the same gene
target_id
sequence-ontology
BUSCO
duplication
3 days ago by
CoLa
• 0
0
votes
1
reply
194
views
doubt about usage of megahit
trinity
megahit
updated 3 days ago by
Istvan Albert
99k • written 3 days ago by
meera
• 0
0
votes
0
replies
125
views
Compute matrix skipping many regions stating not found in compute matrix output
computematrix
Deeptools
3 days ago by
Mehwish
▴ 10
0
votes
0
replies
137
views
is there a way to set colors pallets for glMDSPlot(x)?
Glimma
glMDSPlot
3 days ago by
James
• 0
0
votes
3
replies
804
views
"MethylKit" package for WGBS data
MethylKit
WGBS
updated 3 days ago by
viveksomya123
• 0 • written 2.3 years ago by
shrinka.genetics
▴ 20
0
votes
2
replies
1.5k
views
Does GNOMAD use all LOFTEE LoF filters?
loftee
gnomad
LOF
ensembl
vep
updated 3 days ago by
AMARU
• 0 • written 3.8 years ago by
brismiller
▴ 50
0
votes
0
replies
118
views
bootstraped treemix show no migration event
Treemix
Bootstrap
2 days ago by
reza
▴ 300
0
votes
0
replies
107
views
BioSQL Unable to remove database using server.remove_database
BioSQL
biopython
Mysql
Python
2 days ago by
Navindu
• 0
0
votes
1
reply
204
views
Issue with genetic QC sex check
plink
2 days ago by
kl
▴ 10
0
votes
0
replies
102
views
Should I perform eQTL colocalization for just one of eGenes at a time?
colocalization
coloc
eCaviar
eQTL
2 days ago by
maximal_life
▴ 20
0
votes
3
replies
328
views
Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-voom
RNAseq
differential-gene-expession
limma
batch-effect
updated 1 day ago by
CTLong
▴ 20 • written 3 days ago by
fluke
• 0
0
votes
2
replies
498
views
Understanding gene level copy number data from TCGAbiolinks
CNV
TCGA
updated 20 hours ago by
Zhenyu Zhang
★ 1.1k • written 13 months ago by
billyK
• 0
0
votes
2
replies
130
views
An issue with gtf file (ballgownrsem)
Ballgown
RNA-seq
GTF
RSEM
updated 17 hours ago by
rpolicastro
12k • written 18 hours ago by
cucindarko51
• 0
0
votes
1
reply
74
views
Funannotate iprscan Creates empty file
funannotate
interproscan
fungus
annotation
17 hours ago by
Umer
▴ 50
0
votes
2
replies
233
views
How to identify CG, CHG, or CHH from MeDIP data
MethylationStudy
CHG
CHH
CG
MeDIP
16 hours ago by
Tm
★ 1.1k
94 results • Page
1 of 2
Recent Votes
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Best way to normalize transcript reads data for PCA & correlation and further biostat analysis
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Answer: Best way to normalize transcript reads data for PCA & correlation and further bi
by
Jeremy
▴ 860
Scaling the data will give you Z-scores. This is a standard way of preparing data for PCA. I would also suggest trying a center-log-ratio…
Comment: How to resolve the error of protein lacking a stop codon when using GenomeThread
by
peanut
• 0
Thank you for your answer,but after verifying the protein file, it seems there is no problem. Even if there are missing codons, the program…
Comment: Help with gatk CreateSequenceDictionary
by
Chris
▴ 230
It worked! Thanks Matt!
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i can't really tell you why your code doesn't work if you dont provide it. and, if you describe as much as possible what your goals are, th…
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maybe try?: -R /variant_calling/Desktop/demo/supporting_files/hg38/hg38.fa -O /variant_calling/Desktop/demo/supporting_files/hg38/hg3…
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Looks like you have corrupt or improperly-formatted input. It's expecting to parse a floating-point number where the word "score" appears.…
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The knee plot is just one type of QC. I'd say just proceed with your analysis and see if you observe anything funky (analysis itself is a Q…
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Comment: FastQC without yellow box
by
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• 0
Thank you for your answer.
Comment: FastQC without yellow box
by
lobelino
• 0
My question is Can I trust the statistics of my data I didn't get any yellow boxes, but I got high media values. Why I didn't get any yello…
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by
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78k
The box is the quartiles, the red line the median. Please google how to read a box plot. Your data is good in terms of base quality.
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What's your question?<a href="" title="Text added because biostars parser needs it"></a>
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Deprecated tools don't just stop producing output/errors, that's now how deprecation works.
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