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45 results • Page
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2
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3
replies
1.0k
views
Is it possible to run CibersortX with a very small number of samples?
cibersortx
updated 12 minutes ago by
finch
• 0 • written 19 months ago by
Aspire
▴ 330
0
votes
2
replies
148
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
updated 1 hour ago by
geneontologyhelp
▴ 400 • written 1 day ago by
Pegasus
▴ 100
0
votes
2
replies
46
views
Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis of Spleen Samples from Different Conditions
Seurat
scRNA-Seq
Single-Cell
1 hour ago by
Shukai
• 0
0
votes
1
reply
28
views
Question about samtools view flags (paired reads vs. properly paired reads)
samtools
updated 2 hours ago by
Pierre Lindenbaum
161k • written 2 hours ago by
mrk
• 0
0
votes
2
replies
82
views
z-score of gene set
z-score
scRNA
gene-set
updated 1 hour ago by
Ram
44k • written 4 hours ago by
Hien
• 0
2
votes
1
reply
62
views
converting transcript IDs (Ensembl) to gene symbols in R
RNAseq
updated 2 hours ago by
bk11
★ 2.5k • written 3 hours ago by
ashkan
▴ 160
0
votes
0
replies
30
views
Linking AMR Genes to Taxonomy in Soil Metagenomics
metagenomics
bacteria
wgs
AMR
resistome
updated 2 hours ago by
GenoMax
142k • written 2 hours ago by
LuciaNhu
• 0
0
votes
2
replies
53
views
How can we convert a vcf to fasta, so that I can blast some genes against that whole genome sequences?
blast
fasta
vcf
gene
updated 27 minutes ago by
Ram
44k • written 3 hours ago by
Harshita
• 0
2
votes
0
replies
34
views
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
liftOver
ATAC-seq
Bioinformatics
csaw
3 hours ago by
Rafael Soler
★ 1.2k
0
votes
0
replies
39
views
Job:
PhD position for metagenomics analysis at the University of Udine
metagenomics
bioinformatics
job
3 hours ago by
Fabio Marroni
★ 3.0k
0
votes
0
replies
36
views
How does Kraken2 deal with poor read qualities?
kraken
qiime2
kraken2
qiime
updated 2 hours ago by
GenoMax
142k • written 3 hours ago by
Christopher
• 0
3
votes
5
replies
395
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
4 hours ago by
beantkapoor16
▴ 10
0
votes
1
reply
60
views
DRAGEN gVCF files and joint calling GATK-GenomicsDB
DRAGEN
GenomicsDB
updated 3 hours ago by
DBScan
▴ 300 • written 4 hours ago by
brunomiwa
• 0
0
votes
0
replies
39
views
Last step of metagenome analysis before visualization
metagenome
python
analyis
5 hours ago by
Ayda Ecem
• 0
0
votes
3
replies
94
views
Generating a Bed file from a Fasta file
bedfile
Sequences
Random
NullSeq
updated 4 hours ago by
Pierre Lindenbaum
161k • written 5 hours ago by
pirku
• 0
0
votes
3
replies
1.7k
views
Running STRUCTURE from command line
command
STRUCTURE
unix
updated 5 hours ago by
Arthur
• 0 • written 3.0 years ago by
giulia.trauzzi
▴ 10
1
vote
3
replies
517
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 6 hours ago by
Klaus S
▴ 160 • written 5 weeks ago by
Zeng Hao
▴ 40
0
votes
0
replies
49
views
Calculated LAI is too large
annotation
LAI
assembly
TE
genome
8 hours ago by
Yao
▴ 30
1
vote
1
reply
693
views
Herald:
The Biostar Herald for Monday, November 01, 2021
herald
written 2.6 years ago by
Biostar
2.8k
17
votes
10
replies
7.3k
views
7 follow
T2T-CHM13 "complete" human genome gff/gtf annotation file
genomics
written 3.0 years ago by
noodle
▴ 580
0
votes
0
replies
55
views
How to recover the entire sequence from all_contig_annotations.csv?
VDJ
single-cell
TCR-seq
cellranger
10x
10 hours ago by
dawnyipingzou
• 0
0
votes
4
replies
122
views
Where to find old version of GATK best practice
gatk
1 hour ago by
Zhenyu Zhang
★ 1.2k
0
votes
1
reply
84
views
Nextflow docker: Error response from daemon
sarek
gatk4
docker
nextflow
updated 10 hours ago by
Pierre Lindenbaum
161k • written 11 hours ago by
Peter Chung
▴ 200
0
votes
0
replies
53
views
News:
Online course- Advanced Python for Life Sciences
Python
MachineLearning
Programming
DataVisualisation
11 hours ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
93
views
CreateSeuratObject taking very long
seurat
updated 5 hours ago by
Nitin Narwade
★ 1.6k • written 14 hours ago by
eae6d2e7
• 0
0
votes
0
replies
63
views
Multi-ploid data in ANGSD and NGSadmix
ancestry
diploid
haploid
admixture
16 hours ago by
Christopher
• 0
1
vote
2
replies
164
views
Elbow plot question (scRNA seq data analysis - scanpy tutorial)
scanpy
20 hours ago by
ojaswinipandey
• 0
0
votes
2
replies
150
views
Kraken2 Custom Database non-deterministic results
Metagenomics
kraken2
4 hours ago by
Bjorn
• 0
1
vote
4
replies
258
views
How to find SRA sequences of some fungal whole genome sequences if only Biosample ID is available?
SRA
whole-genome-sequencing
NCBI
updated 22 hours ago by
Ram
44k • written 1 day ago by
Harshita
• 0
2
votes
4
replies
197
views
Filter Genome for Specific Sites
bedtools
updated 22 hours ago by
Ram
44k • written 1 day ago by
Anita
• 0
0
votes
3
replies
216
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 21 hours ago by
marco.barr
▴ 130 • written 1 day ago by
Mohamed Samir
▴ 20
0
votes
0
replies
73
views
News:
Online course: Network analysis in Systems Biology with R/Bioconductor
Bioconductor
Systems-Biology
Network-Analysis
R
updated 22 hours ago by
Ram
44k • written 1 day ago by
carlopecoraro2
★ 2.5k
2
votes
4
replies
362
views
Super ehancers
enhancers
6 hours ago by
Oburah
• 0
0
votes
1
reply
108
views
vcf phasing
beagle
WhatsHap
phasing
updated 5 hours ago by
WouterDeCoster
47k • written 1 day ago by
safeassli
▴ 10
0
votes
0
replies
142
views
How to deal with possibly important predictors omitted during the building of an OLS multivariant linear regression model?
multivariant-linear-regression
updated 22 hours ago by
Ram
44k • written 1 day ago by
JorgeVallejo
▴ 20
1
vote
2
replies
223
views
News:
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
BestTalk
PlatformPresentation
offtopic
updated 9 hours ago by
colindaven
6.4k • written 1 day ago by
Dr.
• 0
1
vote
8
replies
445
views
Add stats to the plot
R
updated 10 hours ago by
marco.barr
▴ 130 • written 2 days ago by
Ghada
• 0
0
votes
0
replies
117
views
problems in installing rDock
rDock
updated 22 hours ago by
Ram
44k • written 2 days ago by
Rodolfo Adrián
• 0
2
votes
3
replies
329
views
Trimming tool
Trimming
updated 22 hours ago by
Ram
44k • written 4 days ago by
GeneC
• 0
4
votes
9
replies
630
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 9 hours ago by
marco.barr
▴ 130 • written 6 days ago by
diqixiaoyaoer
▴ 20
1
vote
6
replies
354
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
6 hours ago by
Umer
▴ 50
0
votes
2
replies
267
views
How can I calculate the OS of each patient?
overall-survival
23 hours ago by
Pedro
• 0
0
votes
5
replies
345
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
20 hours ago by
mavy
▴ 10
4
votes
10
replies
847
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 11 hours ago by
Alex Reynolds
35k • written 25 days ago by
J
▴ 10
19
votes
15
replies
2.3k
views
Forum:
What is the amount of sequencing data produced annually?
data
research
sequencing
updated 8 hours ago by
Mohamed
• 0 • written 8 months ago by
vincenthus
▴ 70
45 results • Page
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Recent Votes
Answer: tensorQTL interaction issue
Answer: converting transcript IDs (Ensembl) to gene symbols in R
Answer: converting transcript IDs (Ensembl) to gene symbols in R
Comment: Trimming tool
Answer: Trimming tool
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
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Recent Replies
Answer: Is it possible to run CibersortX with a very small number of samples?
by
finch
• 0
Hi! I had a very similar issue and it's likely not at all related to your number of samples but to the format of your mixture file! Ciberso…
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
by
Ram
44k
You cannot *convert* a VCF to a FASTA as they have vastly different information content. Please explain your process - what exactly do you …
Comment: Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis o
by
Shukai
• 0
Thank you Ram for the comments! Noted for future posts.
Comment: Where to find old version of GATK best practice
by
Zhenyu Zhang
★ 1.2k
I am looking for diagrams, and step-by-step instructions of how to build my pipelines. I think the github is only helpful if you are a wdl…
Comment: Where to find old version of GATK best practice
by
Zhenyu Zhang
★ 1.2k
oh, this is helpful. Thanks.
Comment: Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis o
by
Ram
44k
1. You can edit your post and add relevant details. There is no need to add separate comments with relevant details especially when it's no…
Answer: Functional enrichment analysis for unique gene IDs
by
geneontologyhelp
▴ 400
If you are looking at producing GO annotations, we currently only recommend InterProScan, and basically only for novel organisms or where t…
Answer: Question about samtools view flags (paired reads vs. properly paired reads)
by
Pierre Lindenbaum
161k
paired reads = the experiment was a paired end assay: each fragment was sequenced on 5' and 3', two FASTQ files are generated by the seque…
Answer: z-score of gene set
by
Matthias Zepper
4.6k
The z-score is a measure of how many standard deviations a particular data point is from the mean of a distribution. A positive z-score ind…
Answer: converting transcript IDs (Ensembl) to gene symbols in R
by
bk11
★ 2.5k
You can do as following: library(biomaRt) # Set up the Ensembl BioMart connection ensembl <- useEnsembl(biomart = "genes",…
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
by
Pierre Lindenbaum
161k
well you try to use FastaAlternateReferenceMaker https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMak…
Comment: z-score of gene set
by
bk11
★ 2.5k
Can you please tell us what will be your propose of z-score calculation?
Comment: DRAGEN gVCF files and joint calling GATK-GenomicsDB
by
DBScan
▴ 300
I think I did it once, but why would you use GATK with DRAGEN gVCF files? If you have a DRAGEN, the iterative gVCF Genotyper does a much fa…
Answer: Practical Haplotype Graph v2 not finding correct paths
by
beantkapoor16
▴ 10
So, I just tested it and it's performing much better now. Most of the haplotype paths are coming from the expected haplotypes (australasica…
Comment: Kraken2 Custom Database non-deterministic results
by
Bjorn
• 0
Thank you!
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