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12,765 results • Page
1 of 256
Sort: Rank
Rank
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Votes
Replies
4
votes
6
replies
327
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In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
1 hour ago by
diqixiaoyaoer
▴ 20
0
votes
0
replies
29
views
constructing pangenome through psvcp
psvcp
pangenome
2 hours ago by
analyst
▴ 50
0
votes
7
replies
74
views
zero TPM for many gene including housekeeping when using kallisto
RNAseq
updated just now by
ATpoint
82k • written 2 hours ago by
ashkan
▴ 160
0
votes
1
reply
43
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
updated 1 hour ago by
dthorbur
★ 2.0k • written 2 hours ago by
Umer
▴ 50
0
votes
1
reply
94
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
updated 4 hours ago by
txema.heredia
▴ 130 • written 12 hours ago by
Ngrin
• 0
3
votes
7
replies
315
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
updated 5 hours ago by
DGTool
▴ 20 • written 23 hours ago by
Gabriel R.
★ 2.9k
0
votes
2
replies
128
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 4 hours ago by
Pierre Lindenbaum
161k • written 10 hours ago by
melissachua90
▴ 70
0
votes
0
replies
44
views
How do I quantify the non-coding transcripts that I have generated after using CPAT,PLEK, and BLAST altogether?
transcript
Quantify
non-coding
6 hours ago by
Varsha
• 0
797
votes
167
replies
143k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.8k • written 7.4 years ago by
Istvan Albert
100k
0
votes
1
reply
115
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 1 hour ago by
GenoMax
142k • written 9 hours ago by
huxiangyulove
• 0
0
votes
0
replies
64
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
12 hours ago by
O.rka
▴ 720
4
votes
5
replies
4.3k
views
Tool:
GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly
Structural-Variation
Variant-Calling
updated 12 hours ago by
dario.garvan
▴ 520 • written 7.2 years ago by
d-cameron
★ 2.9k
0
votes
1
reply
79
views
Help! Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 52 minutes ago by
dthorbur
★ 2.0k • written 13 hours ago by
BATMAN
• 0
0
votes
4
replies
227
views
Merge clusters in Seurat UMAP
seurat
umap
4 hours ago by
kilcdincer
▴ 10
0
votes
0
replies
67
views
Use of ichor CNA
Dog
CNA
genome
18 hours ago by
sainavyav22
• 0
2
votes
2
replies
174
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 16 hours ago by
Ram
43k • written 18 hours ago by
txema.heredia
▴ 130
0
votes
0
replies
82
views
News:
Course on Manual Genome Curation
Genome-Assembly
Pretext-View
Manual-Genome-Curation
updated 13 hours ago by
Ram
43k • written 20 hours ago by
carlopecoraro2
★ 2.5k
4
votes
3
replies
194
views
Details on salmon index
Salmon
1 hour ago by
Lorenzo
• 0
0
votes
0
replies
76
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
20 hours ago by
Jsarria.EEAD
• 0
0
votes
1
reply
125
views
How can I calculate the OS of each patient?
overall-survival
updated 21 hours ago by
ATpoint
82k • written 21 hours ago by
Pedro
• 0
0
votes
1
reply
127
views
mitochondrial genome assembly pipeline
mammals
mitochondrial-genome
updated 21 hours ago by
Ram
43k • written 23 hours ago by
m90
▴ 30
0
votes
0
replies
75
views
cat-bgen fail
bgenix
updated 21 hours ago by
Ram
43k • written 21 hours ago by
lambard
• 0
3
votes
4
replies
253
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
genome
updated 21 hours ago by
Ram
43k • written 1 day ago by
Ali
• 0
3
votes
3
replies
171
views
getting exon coordinates
genomics
updated 21 hours ago by
Ram
43k • written 22 hours ago by
Xbox_27
• 0
0
votes
4
replies
246
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 6 hours ago by
Tony
• 0 • written 1 day ago by
vk
▴ 10
1
vote
5
replies
227
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq
deseq2
updated 13 hours ago by
Ram
43k • written 1 day ago by
manuelmourato25
• 0
3
votes
4
replies
335
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 23 hours ago by
GenoMax
142k • written 1 day ago by
Pierre Lindenbaum
161k
2
votes
11
replies
620
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio
DEG
limma
4 hours ago by
egascon
• 0
1
vote
1
reply
129
views
API kegg - IndexError: list index out of range
kegg
API
updated 9 hours ago by
Nyksubuz
▴ 20 • written 1 day ago by
mirwa.zidi93
• 0
0
votes
0
replies
81
views
Blog:
The Current State and Future Prospects of Long-Read Sequencing
LRS
1 day ago by
Novogene
▴ 420
0
votes
0
replies
84
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
1 day ago by
ebertomeup
• 0
0
votes
3
replies
209
views
Sam file Header problem
Sam
Header
problem
file
updated 5 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
saifulislam99121
• 0
1
vote
4
replies
215
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
offtopic
Degrees
python
updated 13 hours ago by
Ram
43k • written 1 day ago by
kuttibiotech2009
▴ 30
0
votes
1
reply
545
views
scRNAseq quality control weird double curve in nFeature vs nCount plot
scRNA-seq
QC
single
cell
BDRhapsody
analysis
updated 1 day ago by
valdirbarth
▴ 20 • written 12 months ago by
Salomé
• 0
0
votes
0
replies
96
views
select set of intervals that cover a genomic region
GRanges
bed
1 day ago by
ntsopoul
▴ 60
1
vote
1
reply
143
views
Tool:
Collect dispersed executable files and run them by using bingo.
bingo
updated 13 hours ago by
Ram
43k • written 1 day ago by
dwpeng
▴ 10
0
votes
1
reply
124
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
updated 7 hours ago by
Nyksubuz
▴ 20 • written 1 day ago by
Luqman
• 0
2
votes
3
replies
203
views
ggrepel function: geom_text_repel()
ggplot2
ggrepel
R
updated 13 hours ago by
Ram
43k • written 1 day ago by
sooni
▴ 20
0
votes
2
replies
159
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
1 day ago by
mavy
▴ 10
1
vote
1
reply
215
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
1 day ago by
ramiro.barrantes
• 0
2
votes
6
replies
1.9k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML
ncbi
entrez-direct
updated 1 day ago by
Ram
43k • written 3.9 years ago by
millere
• 0
0
votes
1
reply
151
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
updated 1 day ago by
Michael
54k • written 1 day ago by
mgranada3
▴ 30
0
votes
1
reply
139
views
Add line under stat test
stats
R
updated 8 hours ago by
Nyksubuz
▴ 20 • written 1 day ago by
Ghada
• 0
1
vote
5
replies
786
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
0
votes
0
replies
102
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Rodolfo Adrián
• 0
1
vote
3
replies
193
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
updated 1 day ago by
Zhenyu Zhang
★ 1.2k • written 1 day ago by
shpak.max
▴ 50
2
votes
4
replies
259
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 1 day ago by
yura.grabovska
▴ 90 • written 1 day ago by
ev97
▴ 20
1
vote
14
replies
602
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
6 hours ago by
hophuquy0944
• 0
0
votes
4
replies
234
views
Sequencing Depth (Read Depth) Calculations
depth
1 day ago by
LucisTheFather
• 0
0
votes
1
reply
138
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
1 day ago by
asalimih
▴ 60
12,765 results • Page
1 of 256
Recent Votes
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: Details on salmon index
Answer: Generating consensus sequence from bam file
Answer: Short Read Data Genome Assembly
Comment: API kegg - IndexError: list index out of range
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Recent Replies
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ATpoint
82k
Yes, but this is what I am saying: GAPDH in human has at least 6 annotated transcripts. Have you looked at all of them? Maybe that particul…
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@atpoint these are from PBMC. no they are different genes. for example ENST00000229239.10 is GAPDH. in STAR I got a lot of reads aligned …
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@dariober: I have to use kallisto for our downstream pipeline.
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ATpoint
82k
Which celltype is this? Are these transcripts of the same gene, and of which gene?
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@atpoint the question is updated. the first command shows how the index is built.
Comment: Help! Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
Is the *de novo* annotation required for each contig? Reconstructing homologous regions in many genomes can be tricky regardless, but is es…
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
by
diqixiaoyaoer
▴ 20
You can have a look on my answer. I have post it below.
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
by
diqixiaoyaoer
▴ 20
Here is my script that can be used to calculate how much degree that different factors contribute to PCA variance (PC1 and PC2). # …
Comment: Details on salmon index
by
Lorenzo
• 0
Thank you so much for the beautiful explanation. Just one more curiosity. So in the first versions Salmon utilized RapMap to index and then…
Comment: What marks a De-Novo Genome assembly as FAILED?
by
dthorbur
★ 2.0k
I'm a little confused about your experimental design. Are you making 45 different assemblies? Or are all the samples from the same individu…
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ATpoint
82k
You should be stating how you constructed the index, and include the actual lines for the problematic genes from the abundance files. Note …
Comment: zero TPM for many gene including housekeeping when using kallisto
by
dariober
14k
You could try [salmon](https://combine-lab.github.io/salmon/getting_started/) to see if the problem is with kallisto or with the pseudo-ali…
Comment: solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* err
by
GenoMax
142k
> INPUT FILE error: could not open input file /geneInfo.tab Based on the error it appears that the input file you are providing could not …
Answer: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Having duplicate gene symbols is pretty common. Why do you need to work with gene symbols? To compare them to external datasets? Or just fo…
Comment: Merge clusters in Seurat UMAP
by
kilcdincer
▴ 10
It did not help either. But I got the answer [here][1] Thank you! [1]: https://github.com/satijalab/seurat/issues/8902
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