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45 results • Page
1 of 1
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Votes
Replies
0
votes
0
replies
5
views
Problem in getting geo file through GEOQUERY
file
download
Geo
3 minutes ago by
anasjamshed
▴ 120
0
votes
2
replies
44
views
Allele count of 2 for homoplasmic MT variants in VCF
Variant-Calling
GATK
VCF
updated 13 minutes ago by
LChart
3.9k • written 2 hours ago by
Arton
▴ 10
0
votes
1
reply
20
views
downloading chemical database from ChEMBL
ChEMBL
PyRMD
Virtual-Screening
updated just now by
GenoMax
142k • written 56 minutes ago by
s
• 0
0
votes
3
replies
44
views
Where are the illumina adapters on Trimmomatic take from?
rna-seq
trimmomatic
updated 1 hour ago by
GenoMax
142k • written 1 hour ago by
bioinfo
▴ 150
1
vote
1
reply
32
views
Multiplexing for pooled CRISPR screen sequencing
multiplex
CRISPR-screen
Illumina
20 minutes ago by
Tuấn Anh
• 0
2
votes
3
replies
1.1k
views
Is it possible to run CibersortX with a very small number of samples?
cibersortx
updated 3 hours ago by
finch
• 0 • written 19 months ago by
Aspire
▴ 330
1
vote
2
replies
184
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
updated 4 hours ago by
geneontologyhelp
▴ 410 • written 1 day ago by
Pegasus
▴ 100
0
votes
2
replies
104
views
Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis of Spleen Samples from Different Conditions
Seurat
scRNA-Seq
Single-Cell
3 hours ago by
Shukai
• 0
1
vote
3
replies
76
views
Question about samtools view flags (paired reads vs. properly paired reads)
samtools
updated 33 minutes ago by
Pierre Lindenbaum
161k • written 5 hours ago by
mrk
• 0
0
votes
2
replies
119
views
z-score of gene set
z-score
scRNA
gene-set
updated 4 hours ago by
Ram
44k • written 7 hours ago by
Hien
• 0
2
votes
1
reply
90
views
converting transcript IDs (Ensembl) to gene symbols in R
RNA-seq
updated 38 minutes ago by
Ram
44k • written 6 hours ago by
ashkan
▴ 160
0
votes
0
replies
45
views
Linking AMR Genes to Taxonomy in Soil Metagenomics
metagenomics
bacteria
wgs
AMR
resistome
updated 5 hours ago by
GenoMax
142k • written 5 hours ago by
LuciaNhu
• 0
1
vote
2
replies
107
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 3 hours ago by
Ram
44k • written 6 hours ago by
Harshita
• 0
2
votes
0
replies
52
views
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
liftOver
ATAC-seq
csaw
updated 1 hour ago by
Ram
44k • written 6 hours ago by
Rafael Soler
★ 1.2k
0
votes
0
replies
57
views
Job:
PhD position for metagenomics analysis at the University of Udine
metagenomics
updated 1 hour ago by
Ram
44k • written 6 hours ago by
Fabio Marroni
★ 3.0k
0
votes
0
replies
52
views
How does Kraken2 deal with poor read qualities?
kraken
qiime2
kraken2
qiime
updated 5 hours ago by
GenoMax
142k • written 6 hours ago by
Christopher
• 0
3
votes
5
replies
416
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
7 hours ago by
beantkapoor16
▴ 10
0
votes
1
reply
81
views
DRAGEN gVCF files and joint calling GATK-GenomicsDB
DRAGEN
GenomicsDB
updated 6 hours ago by
DBScan
▴ 300 • written 7 hours ago by
brunomiwa
• 0
0
votes
0
replies
49
views
Last step of metagenome analysis before visualization
metagenome
python
analyis
7 hours ago by
Ayda Ecem
• 0
0
votes
3
replies
110
views
Generating a Bed file from a Fasta file
bed
NullSeq
updated 1 hour ago by
Ram
44k • written 8 hours ago by
pirku
• 0
0
votes
3
replies
1.7k
views
Running STRUCTURE from command line
STRUCTURE
updated 1 hour ago by
Ram
44k • written 3.0 years ago by
giulia.trauzzi
▴ 10
1
vote
3
replies
522
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 9 hours ago by
Klaus S
▴ 160 • written 5 weeks ago by
Zeng Hao
▴ 40
0
votes
0
replies
55
views
Calculated LAI is too large
annotation
LAI
assembly
TE
genome
11 hours ago by
Yao
▴ 30
1
vote
1
reply
698
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
61
views
How to recover the entire sequence from all_contig_annotations.csv?
VDJ
single-cell
TCR-seq
cellranger
10x
13 hours ago by
dawnyipingzou
• 0
0
votes
4
replies
166
views
Where to find old version of GATK best practice
gatk
4 hours ago by
Zhenyu Zhang
★ 1.2k
0
votes
1
reply
87
views
Nextflow docker: Error response from daemon
sarek
gatk4
docker
nextflow
updated 13 hours ago by
Pierre Lindenbaum
161k • written 13 hours ago by
Peter Chung
▴ 200
0
votes
0
replies
59
views
News:
Online course- Advanced Python for Life Sciences
Python-Programming
Data-Visualisation
Machine-Learning
updated 1 hour ago by
Ram
44k • written 14 hours ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
99
views
CreateSeuratObject taking very long
seurat
updated 8 hours ago by
Nitin Narwade
★ 1.6k • written 17 hours ago by
eae6d2e7
• 0
0
votes
0
replies
67
views
Multi-ploid data in ANGSD and NGSadmix
ancestry
diploid
haploid
admixture
19 hours ago by
Christopher
• 0
1
vote
2
replies
171
views
Elbow plot question (scRNA seq data analysis - scanpy tutorial)
scanpy
23 hours ago by
ojaswinipandey
• 0
0
votes
2
replies
164
views
Kraken2 Custom Database non-deterministic results
Metagenomics
kraken2
7 hours ago by
Bjorn
• 0
3
votes
5
replies
387
views
Super ehancers
enhancers
updated 2 hours ago by
jared.andrews07
★ 17k • written 19 days ago by
Oburah
• 0
0
votes
1
reply
117
views
vcf phasing
beagle
WhatsHap
phasing
updated 8 hours ago by
WouterDeCoster
47k • written 1 day ago by
safeassli
▴ 10
1
vote
2
replies
225
views
News:
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
BestTalk
PlatformPresentation
offtopic
updated 12 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 13 hours ago by
marco.barr
▴ 130 • written 2 days ago by
Ghada
• 0
1
vote
2
replies
363
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 2 hours ago by
finch
• 0 • written 3 months ago by
star
▴ 10
4
votes
9
replies
637
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 11 hours ago by
marco.barr
▴ 130 • written 6 days ago by
diqixiaoyaoer
▴ 20
1
vote
6
replies
357
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
9 hours ago by
Umer
▴ 50
0
votes
5
replies
346
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
23 hours ago by
mavy
▴ 10
1
vote
4
replies
217
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
10 minutes ago by
shpak.max
▴ 50
1
vote
4
replies
303
views
Filtering VCF files based on VAF giving incorrect results
GATK
picard
VCF
bcftools
updated 1 hour ago by
Ram
44k • written 6 days ago by
Arton
▴ 10
4
votes
10
replies
848
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 14 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 11 hours ago by
Mohamed
• 0 • written 8 months ago by
vincenthus
▴ 70
45 results • Page
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Answer: Question about samtools view flags (paired reads vs. properly paired reads)
Answer: Functional enrichment analysis for unique gene IDs
Comment: Super ehancers
Comment: Why does assigning genes with biomart give me different values than using a tran
Comment: Multiplexing for pooled CRISPR screen sequencing
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
Answer: Differential Expression with limma: Contrast and Design Matrix, combinatorial ap
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Recent Replies
Comment: downloading chemical database from ChEMBL
by
GenoMax
142k
How about following https://www.ebi.ac.uk/chembl/web_components/explore/activities/ --> Select a compound --> Related Targets button --> D…
Comment: Genotyping sites with N in reference genome
by
shpak.max
▴ 50
As a follow-up, is it possible to get a variant call if rather than N, I have one of the ambiguity codes (e.g. R, Y, B etc) in the referenc…
Answer: Allele count of 2 for homoplasmic MT variants in VCF
by
LChart
3.9k
The GATK (and afaik every caller that I know) treats every contig of the reference as having the same ploidy (so all haploid, all diploid, …
Comment: Where are the illumina adapters on Trimmomatic take from?
by
GenoMax
142k
Use the sequence Illumina recommends for the specific kit.
Comment: Question about samtools view flags (paired reads vs. properly paired reads)
by
Pierre Lindenbaum
161k
> Thanks. What determines what constitutes a good distance? I think tools like BWA use the median distance for each chunk of processed d…
Comment: Where are the illumina adapters on Trimmomatic take from?
by
bioinfo
▴ 150
Thank you for the explanation. Is it more appropriate then to use the sequence from the illumina documentation or the one from the github?
Comment: Question about samtools view flags (paired reads vs. properly paired reads)
by
mrk
• 0
Thanks. What determines what constitutes a good distance? I have some targeted panel data and looking at flagstat, almost all reads are pai…
Answer: Where are the illumina adapters on Trimmomatic take from?
by
GenoMax
142k
Illumina indexed adapters share a core sequence at the beginning which is what is indicated in your link. Trimming programs will remove seq…
Comment: Allele count of 2 for homoplasmic MT variants in VCF
by
Ram
44k
Please stop using `bioinformatics` as a tag unless your post is about the field of bioinformatics itself.
Comment: Multiplexing for pooled CRISPR screen sequencing
by
GenoMax
142k
> If we switch to pair-end sequencing with dual-index barcode You can use dual-indexing with single end reads. You don't need to do paired…
Comment: Super ehancers
by
jared.andrews07
★ 17k
That is not valid GFF format, so that is probably going to be problematic. See the [GFF spec](https://github.com/The-Sequence-Ontology/Spec…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
finch
• 0
Hey! I had this issue and I think I can help- could you take a screenshot of the .txt file opened in the notepad?
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.
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