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116,993 results • Page
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Sort: Rank
Rank
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Votes
Replies
1
vote
3
replies
87
views
Help! Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
just now by
BATMAN
• 0
0
votes
0
replies
11
views
Understanding behaviour of SCTransform in Seurat
Seurat
scRNASeq
normalization
updated 20 minutes ago by
GenoMax
142k • written 43 minutes ago by
yura.grabovska
▴ 90
4
votes
7
replies
356
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 44 minutes ago by
marco.barr
▴ 130 • written 1 day ago by
diqixiaoyaoer
▴ 20
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
0
replies
39
views
constructing pangenome through psvcp
psvcp
pangenome
3 hours ago by
analyst
▴ 50
1
vote
8
replies
112
views
zero TPM for many gene including housekeeping when using kallisto
RNAseq
16 minutes ago by
ashkan
▴ 160
0
votes
1
reply
59
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
updated 2 hours ago by
dthorbur
★ 2.0k • written 3 hours ago by
Umer
▴ 50
0
votes
1
reply
104
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
updated 4 hours ago by
txema.heredia
▴ 130 • written 13 hours ago by
Ngrin
• 0
3
votes
9
replies
332
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
11 minutes ago by
Gabriel R.
★ 2.9k
0
votes
2
replies
136
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 5 hours ago by
Pierre Lindenbaum
161k • written 11 hours ago by
melissachua90
▴ 70
0
votes
0
replies
49
views
How do I quantify the non-coding transcripts that I have generated after using CPAT,PLEK, and BLAST altogether?
transcript
Quantify
non-coding
7 hours ago by
Varsha
• 0
0
votes
1
reply
133
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 2 hours ago by
GenoMax
142k • written 10 hours ago by
huxiangyulove
• 0
0
votes
0
replies
67
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
13 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 13 hours ago by
dario.garvan
▴ 520 • written 7.2 years ago by
d-cameron
★ 2.9k
0
votes
4
replies
236
views
Merge clusters in Seurat UMAP
seurat
umap
5 hours ago by
kilcdincer
▴ 10
0
votes
0
replies
71
views
Use of ichor CNA
Dog
CNA
genome
19 hours ago by
sainavyav22
• 0
2
votes
2
replies
176
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 17 hours ago by
Ram
43k • written 19 hours ago by
txema.heredia
▴ 130
0
votes
0
replies
84
views
News:
Course on Manual Genome Curation
Genome-Assembly
Pretext-View
Manual-Genome-Curation
updated 14 hours ago by
Ram
43k • written 21 hours ago by
carlopecoraro2
★ 2.5k
4
votes
4
replies
204
views
Details on salmon index
Salmon
updated just now by
Rob
6.6k • written 1 day ago by
Lorenzo
• 0
0
votes
0
replies
77
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
21 hours ago by
Jsarria.EEAD
• 0
0
votes
1
reply
126
views
How can I calculate the OS of each patient?
overall-survival
updated 22 hours ago by
ATpoint
82k • written 22 hours ago by
Pedro
• 0
1
vote
1
reply
130
views
mitochondrial genome assembly pipeline
mammals
mitochondrial-genome
updated 22 hours ago by
Ram
43k • written 1 day ago by
m90
▴ 30
0
votes
0
replies
76
views
cat-bgen fail
bgenix
updated 22 hours ago by
Ram
43k • written 22 hours ago by
lambard
• 0
3
votes
4
replies
254
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
genome
updated 22 hours ago by
Ram
43k • written 1 day ago by
Ali
• 0
3
votes
3
replies
173
views
getting exon coordinates
genomics
updated 22 hours ago by
Ram
43k • written 23 hours ago by
Xbox_27
• 0
0
votes
4
replies
249
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 7 hours ago by
Tony
• 0 • written 1 day ago by
vk
▴ 10
1
vote
5
replies
229
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq
deseq2
updated 14 hours ago by
Ram
43k • written 1 day ago by
manuelmourato25
• 0
3
votes
4
replies
336
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Pierre Lindenbaum
161k
2
votes
11
replies
628
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
5 hours ago by
egascon
• 0
1
vote
1
reply
132
views
API kegg - IndexError: list index out of range
kegg
API
updated 10 hours ago by
Nyksubuz
▴ 20 • written 1 day ago by
mirwa.zidi93
• 0
0
votes
0
replies
82
views
Blog:
The Current State and Future Prospects of Long-Read Sequencing
LRS
1 day ago by
Novogene
▴ 420
0
votes
0
replies
85
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
1 day ago by
ebertomeup
• 0
0
votes
3
replies
214
views
Sam file Header problem
Sam
Header
problem
file
updated 6 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
saifulislam99121
• 0
1
vote
4
replies
218
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
offtopic
Degrees
python
updated 14 hours ago by
Ram
43k • written 2 days ago by
kuttibiotech2009
▴ 30
0
votes
1
reply
546
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
98
views
select set of intervals that cover a genomic region
GRanges
bed
1 day ago by
ntsopoul
▴ 60
1
vote
1
reply
146
views
Tool:
Collect dispersed executable files and run them by using bingo.
bingo
updated 14 hours ago by
Ram
43k • written 1 day ago by
dwpeng
▴ 10
0
votes
1
reply
125
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
updated 8 hours ago by
Nyksubuz
▴ 20 • written 1 day ago by
Luqman
• 0
2
votes
3
replies
206
views
ggrepel function: geom_text_repel()
ggplot2
ggrepel
R
updated 14 hours ago by
Ram
43k • written 1 day ago by
sooni
▴ 20
0
votes
2
replies
161
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
1 day ago by
mavy
▴ 10
1
vote
1
reply
216
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
152
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
141
views
Add line under stat test
stats
R
updated 9 hours ago by
Nyksubuz
▴ 20 • written 1 day ago by
Ghada
• 0
1
vote
5
replies
787
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
0
votes
0
replies
103
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
194
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
262
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
606
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
7 hours ago by
hophuquy0944
• 0
0
votes
4
replies
236
views
Sequencing Depth (Read Depth) Calculations
depth
1 day ago by
LucisTheFather
• 0
116,993 results • Page
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Recent Votes
Sequence Alignment from Scratch with BWA
Answer: mitochondrial genome assembly pipeline
Comment: Help! Reconstruction of locus, order contigs
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
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Recent Replies
Comment: Details on salmon index
by
Rob
6.6k
Hi Lorenzo, That is correct. The initial version of salmon used the RapMap index explained above. When we published the selective align…
Answer: Help! Reconstruction of locus, order contigs
by
BATMAN
• 0
Is there any way to get the ordering of each genome in .gbk format from progressiveMauve?
Comment: Help! Reconstruction of locus, order contigs
by
BATMAN
• 0
Thanks for your reply, my idea is not to have to write it down. What I have is an alignment of the .gbk from the progressiveMauve. It would…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
I did some digging aroumd, no static binary. Plus it seems you need to roll your own program.
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
We tested it, however, it does not seem to produce a fast a file of the results or anything that we can easily parse. It produces a CIGAR a…
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@atpoint yes but for example for the kallisto results I have expression for 2080 genes (transcripts) and the rest are 0 but in my STAR resu…
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
by
marco.barr
▴ 130
great team work! why can't you access and do the calculation for the other components too? can't you extract the information from the other…
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). # …
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