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21 results • Page
1 of 1
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
12
views
Annovar using R package
Annovar
gnomAD
R
35 minutes ago by
DKA
▴ 40
0
votes
0
replies
36
views
Finding orthologs between genome error
OMA
OMAbrowser
3 hours ago by
hemantcnaik
• 0
0
votes
0
replies
55
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 1 hour ago by
Ram
43k • written 6 hours ago by
glaciya2018
• 0
0
votes
0
replies
62
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
6 hours ago by
pramach1
▴ 40
0
votes
1
reply
80
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 5 hours ago by
Sofia
• 0 • written 9 hours ago by
mawigoj318
• 0
0
votes
0
replies
67
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
10 hours ago by
salias
• 0
0
votes
2
replies
126
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 1 hour ago by
Ram
43k • written 11 hours ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
57
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 1 hour ago by
Ram
43k • written 11 hours ago by
newuser2024
• 0
0
votes
0
replies
50
views
Network Alignment
plugin
Cytoscape
CytoMCS
12 hours ago by
Akash D
▴ 40
0
votes
1
reply
98
views
alignment result
RNA-seq
samtools
hisat2
updated 1 hour ago by
Ram
43k • written 12 hours ago by
ahmad.sajad4541
• 0
0
votes
0
replies
51
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 1 hour ago by
Ram
43k • written 14 hours ago by
Jeyong
• 0
0
votes
0
replies
67
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
21 hours ago by
Kash
▴ 110
0
votes
1
reply
105
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 16 hours ago by
Mensur Dlakic
★ 27k • written 22 hours ago by
benguyarenbeyaz98
• 0
0
votes
2
replies
187
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 1 hour ago by
Ram
43k • written 23 hours ago by
v.berriosfarias
▴ 140
2
votes
9
replies
777
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 19 hours ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
10
replies
343
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
17 hours ago by
atowns21
• 0
0
votes
5
replies
255
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
9 hours ago by
njornet
▴ 20
1
vote
3
replies
224
views
some error in building kraken2 database
metagenome
kraken2
18 hours ago by
Art1ess
• 0
0
votes
1
reply
184
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 22 hours ago by
Istvan Albert
100k • written 1 day ago by
qudrat.nii
▴ 10
2
votes
4
replies
236
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
11 hours ago by
samuelkalandarov2002
▴ 10
0
votes
6
replies
422
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 11 hours ago by
gv
• 0 • written 23 days ago by
Srinka
▴ 20
21 results • Page
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Recent Votes
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
Comment: To get p-values for the TPM
A: Where To Download Pam50 Gene Set?
A: Where To Download Pam50 Gene Set?
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Recent Replies
Comment: Adding CB tag to bam file
by
swbarnes2
14k
I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
Even if this was real data, the tiny numbers for the PC1 and PC2 indicate that the differences between the samples are all absolutely tiny.…
Comment: Creating Synthetic Sequences for a ML Model
by
biochugs
• 0
Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
DKA
▴ 40
I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
Comment: PCA plot (Suggestions Needed)
by
Mensur Dlakic
★ 27k
Everything that @f1f58aed said, plus that there may be no data manipulation that will give you the clusters you expected. Sometimes there a…
Answer: Creating Synthetic Sequences for a ML Model
by
Mensur Dlakic
★ 27k
It is a good idea, though I don't see how it would work in practice. I think you will encounter at least additional problem on top of da…
Answer: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
Right now, the WT samples are clustering together, but you have one mutant sample off by itself, which could be an outlier. How did you sc…
Comment: Adding CB tag to bam file
by
GenoMax
141k
@yokofakun had written this: https://www.biostars.org/p/336965/ https://github.com/ruqianl/appendCB may also be useful.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
GenoMax
141k
Please post information about your tool as a `tools` category post. Don't wait/ask other users to ask you.
Comment: Adding CB tag to bam file
by
Maria
• 0
Sorry for the delay in my answer, I got sidetracked. I am using ```samtools addreplacerg -r "@RG\tID:$cell" -o $cell.bam -h $LINE``` bu…
Answer: Troubleshooting RNA-seq data with DNA contamination
by
haibol2017
▴ 10
We just developed a R package to tackle this problem. Do you have stranded or unstranded RNA-seq data contaminated with gDNA? If you wou…
Comment: How to trim transcripts using information from NCBI contamination screen report
by
GenoMax
141k
`bbduk.sh` can use the transcripts as input. There is a `adapters.fa` included in the `resources` directory of the distribution. You can do…
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
Cross posted here (including the code used to make up the counts): https://support.bioconductor.org/p/9157911/#9157959
Comment: To get p-values for the TPM
by
swbarnes2
14k
RSEM returns a kind of p-value if you run it with the "prior-enhanced" option. Did you do that? Are you completely sure that's the value y…
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