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116,988 results • Page
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Tutorial:
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
1 hour ago by
huxiangyulove
• 0
0
votes
0
replies
29
views
How to generate table_annovar from VCF input?
vcf
annovar
2 hours ago by
melissachua90
▴ 70
0
votes
0
replies
36
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
4 hours ago by
Ngrin
• 0
0
votes
0
replies
34
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
4 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 4 hours ago by
dario.garvan
▴ 520 • written 7.2 years ago by
d-cameron
★ 2.9k
0
votes
0
replies
38
views
Help! Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
4 hours ago by
BATMAN
• 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
3
replies
154
views
Merge clusters in Seurat UMAP
seurat
umap
updated 5 hours ago by
Ram
43k • written 7 hours ago by
kilcdincer
▴ 10
0
votes
0
replies
53
views
Use of ichor CNA
Dog
CNA
genome
9 hours ago by
sainavyav22
• 0
2
votes
2
replies
148
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 7 hours ago by
Ram
43k • written 10 hours ago by
txema.heredia
▴ 130
0
votes
0
replies
63
views
News:
Course on Manual Genome Curation
Genome-Assembly
Pretext-View
Manual-Genome-Curation
updated 5 hours ago by
Ram
43k • written 11 hours ago by
carlopecoraro2
★ 2.5k
3
votes
2
replies
164
views
Details on salmon index
Salmon
updated 12 hours ago by
Rob
6.6k • written 18 hours ago by
Lorenzo
• 0
0
votes
0
replies
60
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
12 hours ago by
Jsarria.EEAD
• 0
0
votes
1
reply
109
views
How can I calculate the OS of each patient?
overall-survival
updated 12 hours ago by
ATpoint
82k • written 13 hours ago by
Pedro
• 0
0
votes
1
reply
110
views
mitochondrial genome assembly pipeline
mammals
mitochondrial-genome
updated 13 hours ago by
Ram
43k • written 15 hours ago by
m90
▴ 30
0
votes
0
replies
59
views
cat-bgen fail
bgenix
updated 13 hours ago by
Ram
43k • written 13 hours ago by
lambard
• 0
3
votes
4
replies
237
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
genome
updated 13 hours ago by
Ram
43k • written 20 hours ago by
Ali
• 0
3
votes
3
replies
156
views
getting exon coordinates
genomics
updated 13 hours ago by
Ram
43k • written 14 hours ago by
Xbox_27
• 0
3
votes
5
replies
225
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
updated 4 hours ago by
GenoMax
142k • written 14 hours ago by
Gabriel R.
★ 2.9k
0
votes
3
replies
202
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 5 hours ago by
Ram
43k • written 1 day ago by
vk
▴ 10
1
vote
5
replies
206
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq
deseq2
updated 5 hours ago by
Ram
43k • written 18 hours ago by
manuelmourato25
• 0
3
votes
4
replies
319
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 14 hours ago by
GenoMax
142k • written 18 hours ago by
Pierre Lindenbaum
161k
1
vote
9
replies
530
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
updated 8 hours ago by
swbarnes2
14k • written 1 day ago by
egascon
• 0
0
votes
1
reply
82
views
API kegg - IndexError: list index out of range
kegg
API
updated 50 minutes ago by
Nyksubuz
▴ 10 • written 19 hours ago by
mirwa.zidi93
• 0
0
votes
0
replies
69
views
Blog:
The Current State and Future Prospects of Long-Read Sequencing
LRS
20 hours ago by
Novogene
▴ 420
0
votes
0
replies
73
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
21 hours ago by
ebertomeup
• 0
0
votes
2
replies
141
views
Sam file Header problem
Sam
Header
problem
file
2 hours ago by
saifulislam99121
• 0
1
vote
4
replies
202
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
offtopic
Degrees
python
updated 5 hours ago by
Ram
43k • written 1 day ago by
kuttibiotech2009
▴ 30
0
votes
1
reply
531
views
scRNAseq quality control weird double curve in nFeature vs nCount plot
scRNA-seq
QC
single
cell
BDRhapsody
analysis
updated 23 hours ago by
valdirbarth
▴ 20 • written 12 months ago by
Salomé
• 0
0
votes
0
replies
83
views
select set of intervals that cover a genomic region
GRanges
bed
23 hours ago by
ntsopoul
▴ 60
1
vote
1
reply
121
views
Tool:
Collect dispersed executable files and run them by using bingo.
bingo
updated 5 hours ago by
Ram
43k • written 1 day ago by
dwpeng
▴ 10
0
votes
0
replies
75
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
1 day ago by
Luqman
• 0
1
vote
3
replies
180
views
ggrepel function: geom_text_repel()
ggplot2
ggrepel
R
updated 5 hours ago by
Ram
43k • written 1 day ago by
sooni
▴ 20
0
votes
2
replies
142
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
21 hours ago by
mavy
▴ 10
1
vote
1
reply
201
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
1 day ago by
ramiro.barrantes
• 0
1
vote
4
replies
287
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
11 hours ago by
diqixiaoyaoer
▴ 10
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
134
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
updated 19 hours ago by
Michael
54k • written 1 day ago by
mgranada3
▴ 30
0
votes
1
reply
100
views
Add line under stat test
stats
R
updated 26 minutes ago by
Nyksubuz
▴ 10 • written 1 day ago by
Ghada
• 0
1
vote
5
replies
777
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
0
votes
0
replies
88
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
181
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
248
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
13
replies
533
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 8 hours ago by
Ram
43k • written 1 day ago by
hophuquy0944
• 0
0
votes
4
replies
221
views
Sequencing Depth (Read Depth) Calculations
depth
1 day ago by
LucisTheFather
• 0
0
votes
1
reply
127
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
1 day ago by
asalimih
▴ 60
0
votes
0
replies
99
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
1 day ago by
jway
• 0
2
votes
2
replies
173
views
Cannot install bwa-mem2 via conda
conda
mamba
python
updated 13 hours ago by
Ram
43k • written 1 day ago by
jsmith120f
• 0
2
votes
2
replies
186
views
genome finishing
finishing
genome
updated 1 day ago by
nd48
▴ 20 • written 1 day ago by
trezini
• 0
1
vote
5
replies
212
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos
atacseq
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
biology_inform
▴ 50
116,988 results • Page
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Recent Votes
Forward And Reverse Strand Conventions
Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
Comment: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Answer: Details on salmon index
ATAC-seq sample normalization
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
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Recent Replies
Comment: Add line under stat test
by
Nyksubuz
▴ 10
You could use [this][1] [1]: https://ggplot2.tidyverse.org/reference/geom_segment.html
Comment: API kegg - IndexError: list index out of range
by
Nyksubuz
▴ 10
It might be because the gene symbol is not found in the KEGG database. Add some extra error handling before parsing the results or do a man…
Comment: Sam file Header problem
by
saifulislam99121
• 0
Thank you for your reply. I am not very much sure about this RG. Can you explain me a bit?
Comment: GRIDSS: the Genomic Rearrangement IDentification Software Suite
by
dario.garvan
▴ 520
It seems that Alexandrov's [structural variant and copy number signatures][1] estimated by the [SigProfiler software ecosystem][2] aren't c…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
GenoMax
142k
Then you may want to see if a program like `lastz` ([**LINK**][1]) may be useful. [1]: https://github.com/lastz/lastz
Comment: Collect dispersed executable files and run them by using bingo.
by
Ram
43k
What is the purpose of this tool? I have `~/bin` in my $PATH and I soft-link all executables I need to that location so why install a new t…
Comment: Merge clusters in Seurat UMAP
by
bk11
★ 2.4k
Can you try this? library(dplyr) seuratobj@meta.data <- seuratobj@meta.data %>% mutate(seurat_clusters = recode(seurat_clu…
Comment: Merge clusters in Seurat UMAP
by
kilcdincer
▴ 10
Thank you for the response but it does not change anything.
Comment: Merge clusters in Seurat UMAP
by
bk11
★ 2.4k
I have not tested but you could try something like below- seuratobj$seurat_clusters[seuratobj$seurat_clusters==5]=0 seuratobj$seur…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
I know about it, isn't there a simple C++ static binary?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
needle is great! but it does not handle sequences of 100k or so.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Ram
43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
by
txema.heredia
▴ 130
The point is that you need to feed the ambient algorithm a clustering list as input. This way, it checks for genes present in the soup vs g…
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
swbarnes2
14k
Wait, so the magnitudes of the PCs are in the thousands? That's not normal for RNASeq.
Comment: Help with VG Toolkit: VCF Output is Empty
by
Jordan M Eizenga
▴ 460
What do you get if you use `vg stats -a` on the GAM file?
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