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43 results • Page
1 of 1
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Views
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1
vote
4
replies
110
views
Help! Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 4 minutes ago by
dthorbur
★ 2.0k • written 14 hours ago by
BATMAN
• 0
0
votes
0
replies
12
views
Understanding behaviour of SCTransform in Seurat
Seurat
scRNASeq
normalization
updated 50 minutes ago by
GenoMax
142k • written 1 hour ago by
yura.grabovska
▴ 90
4
votes
7
replies
357
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 1 hour ago by
marco.barr
▴ 130 • written 1 day ago by
diqixiaoyaoer
▴ 20
0
votes
0
replies
39
views
constructing pangenome through psvcp
psvcp
pangenome
3 hours ago by
analyst
▴ 50
1
vote
8
replies
127
views
zero TPM for many gene including housekeeping when using kallisto
RNAseq
34 minutes ago by
ashkan
▴ 160
0
votes
1
reply
64
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
updated 2 hours ago by
dthorbur
★ 2.0k • written 4 hours ago by
Umer
▴ 50
0
votes
1
reply
106
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
updated 5 hours ago by
txema.heredia
▴ 130 • written 14 hours ago by
Ngrin
• 0
3
votes
9
replies
335
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
31 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 12 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
138
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 3 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
14 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 14 hours ago by
dario.garvan
▴ 520 • written 7.2 years ago by
d-cameron
★ 2.9k
0
votes
4
replies
237
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
177
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 17 hours ago by
Ram
43k • written 20 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
5
votes
4
replies
215
views
Details on salmon index
Salmon
updated 24 minutes ago 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
132
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
77
views
cat-bgen fail
bgenix
updated 22 hours ago by
Ram
43k • written 23 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 1 day 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 8 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
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
6 hours ago by
egascon
• 0
1
vote
1
reply
134
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
3
replies
215
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
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
1
reply
141
views
Add line under stat test
stats
R
updated 10 hours ago by
Nyksubuz
▴ 20 • written 1 day ago by
Ghada
• 0
1
vote
14
replies
607
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
7 hours ago by
hophuquy0944
• 0
2
votes
2
replies
181
views
Cannot install bwa-mem2 via conda
conda
mamba
python
updated 23 hours ago by
Ram
43k • written 1 day ago by
jsmith120f
• 0
0
votes
1
reply
147
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
updated 23 hours ago by
GenoMax
142k • written 2 days ago by
Lélé
▴ 10
0
votes
4
replies
244
views
calculating genomic coverage/ base overlap in R
genomics
updated 22 hours ago by
Ram
43k • written 2 days ago by
Xbox_27
• 0
1
vote
5
replies
256
views
Annotating file using bcftools
annotation
plink
bcftools
23 hours ago by
kl
▴ 10
1
vote
2
replies
222
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
22 hours ago by
bioinfo
▴ 150
1
vote
3
replies
268
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 19 hours ago by
GenoMax
142k • written 3 days ago by
ohtang7
▴ 40
1
vote
1
reply
184
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 18 hours ago by
Jordan M Eizenga
▴ 460 • written 11 days ago by
sarumonsus
▴ 10
1
vote
3
replies
795
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon
chromosome
polish
genome
draft
updated 19 hours ago by
sansan_96
▴ 90 • written 2.7 years ago by
boymin2020
▴ 80
43 results • Page
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Recent Votes
Answer: Details on salmon index
Comment: zero TPM for many gene including housekeeping when using kallisto
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
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Recent Replies
Comment: Help! Reconstruction of locus, order contigs
by
GenoMax
142k
Please use `ADD REPLY/ADD COMMENT` when responding to existing content. `SUBMIT ANSWER` is for new answers to the original question.
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…
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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