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Limit : this year
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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
3
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
just now by
ohtang7
▴ 40
0
votes
0
replies
6
views
What does the 'E%' represent in BUSCO results?
BUSCO
10 minutes ago by
林明德
• 0
0
votes
1
reply
27
views
Filtering based on alternate allelic balance
GATK
Bioinformatics
Filter
VCF
20 minutes ago by
Arton
• 0
0
votes
0
replies
11
views
Biomart issue, why so few 3'utrs?
utr
biomart
31 minutes ago by
RNAseqer
▴ 270
0
votes
2
replies
28
views
Help with IGV abbreviation
Genome
browser
updated 28 minutes ago by
Mathew
▴ 120 • written 38 minutes ago by
GeneC
• 0
0
votes
1
reply
55
views
How to process Bulk WES data?
WES
WGS
updated 2 hours ago by
GenoMax
142k • written 3 hours ago by
wyuan37
• 0
0
votes
1
reply
47
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 1 hour ago by
GenoMax
142k • written 4 hours ago by
cedric.blais
• 0
0
votes
2
replies
347
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
4 hours ago by
David Langenberger
11k
0
votes
1
reply
56
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 2 hours ago by
Ram
43k • written 4 hours ago by
eking28
• 0
1
vote
4
replies
329
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 4 hours ago by
GenoMax
142k • written 5 days ago by
Prawesh
• 0
1
vote
3
replies
296
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
5 hours ago by
kalavattam
▴ 190
795
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
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
1
reply
124
views
How to interpret infinite odds ratio?
statistics
updated 6 hours ago by
bhumm
▴ 140 • written 11 hours ago by
Lukas
• 0
1
vote
2
replies
91
views
Duplicated sequence samtools
bowtie2
samtools
updated 6 hours ago by
GenoMax
142k • written 7 hours ago by
Moinuddin
• 0
0
votes
0
replies
42
views
reference-free assembly error assessment tools
assembly
7 hours ago by
lagartija
▴ 160
1
vote
2
replies
126
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
updated 7 hours ago by
lagartija
▴ 160 • written 12 hours ago by
Esraa
• 0
1
vote
0
replies
46
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
8 hours ago by
J.
▴ 10
0
votes
0
replies
59
views
Herald:
The Biostar Herald for Monday, May 13, 2024
herald
8 hours ago by
Biostar
2.7k
0
votes
1
reply
71
views
Splitting Seurat object by sample layers
seurat
updated 2 hours ago by
Ram
43k • written 8 hours ago by
kilcdincer
▴ 10
0
votes
3
replies
107
views
Galaxy StringTie error
stringtie
galaxy
updated 58 minutes ago by
Mathew
▴ 120 • written 8 hours ago by
trkfs
• 0
0
votes
0
replies
50
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
10 hours ago by
atariw
▴ 10
0
votes
1
reply
98
views
Mouse ribosome sequences in fasta format
fasta
mm10
rRNA
updated 11 hours ago by
GenoMax
142k • written 21 hours ago by
octpus616
▴ 100
0
votes
1
reply
82
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 11 hours ago by
Juke34
8.6k • written 11 hours ago by
Vijith
▴ 30
0
votes
1
reply
97
views
consensus sequence calling
consensus
updated 8 hours ago by
bk11
★ 2.4k • written 12 hours ago by
Ghada
• 0
0
votes
3
replies
121
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 2 hours ago by
Ram
43k • written 13 hours ago by
yau
• 0
3
votes
2
replies
212
views
imputation through beagle
panel
beagle
reference
imputation
7 hours ago by
analyst
▴ 50
0
votes
0
replies
50
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
12 hours ago by
JACKY
▴ 140
0
votes
1
reply
356
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
updated 13 hours ago by
aw7
▴ 280 • written 24 days ago by
abhishekghadge
• 0
1
vote
1
reply
166
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
updated 13 hours ago by
aw7
▴ 280 • written 4 days ago by
Zeng Hao
▴ 40
0
votes
0
replies
62
views
Reference panel of normals for ensembl named refgenome
Mutect2
14 hours ago by
gernophil
▴ 80
1
vote
0
replies
57
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
14 hours ago by
tomas4482
▴ 400
2
votes
3
replies
205
views
BWA alignment
Samtools
bam
15 hours ago by
Vahid
• 0
3
votes
2
replies
130
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 15 hours ago by
ATpoint
82k • written 15 hours ago by
jennyp0706
• 0
0
votes
1
reply
126
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence
university
assembly
protein
genomics
updated 16 hours ago by
Philipp Bayer
8.4k • written 1 day ago by
samRayne
• 0
0
votes
1
reply
210
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 2 hours ago by
Ram
43k • written 4 days ago by
Nikki
• 0
2
votes
13
replies
2.8k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 18 hours ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
0
votes
1
reply
162
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
updated 18 hours ago by
chrchang523
10k • written 5 days ago by
analyst
▴ 50
0
votes
0
replies
77
views
lncRNA
tcga
lncrna
19 hours ago by
jain72744
▴ 10
0
votes
1
reply
207
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
updated 1 day ago by
Zhenyu Zhang
★ 1.2k • written 3 days ago by
jain72744
▴ 10
2
votes
5
replies
513
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 1 day ago by
arctic
▴ 40 • written 10 days ago by
M.
▴ 30
1
vote
2
replies
296
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq
limma
RNA-seq
removeBatchEffect
batch-effect
updated 9 hours ago by
Ram
43k • written 1 day ago by
t.fortunato.asquini
• 0
2
votes
1
reply
227
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
updated 1 day ago by
pjb39
▴ 210 • written 3 days ago by
beantkapoor16
▴ 10
0
votes
2
replies
179
views
Output file of samtools flagstat empty
samtools-flagstat
updated 15 hours ago by
colindaven
6.4k • written 1 day ago by
ramendra.sarma
• 0
0
votes
0
replies
94
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
eigencorplot
PCAtools
deseq2
pca
1 day ago by
BioinfGuru
★ 1.7k
2
votes
8
replies
311
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
Matteo Ungaro
▴ 100
0
votes
0
replies
107
views
News:
Online course: An Introduction to Nanopore Direct RNA Sequencing
Nanopore
RNAseq
1 day ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
215
views
input file in rmats
rmats
updated 1 day ago by
Mathew
▴ 120 • written 3 days ago by
Lambodarswain316
• 0
2
votes
3
replies
271
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 40 minutes ago by
Mathew
▴ 120 • written 2 days ago by
Christopher
• 0
6
votes
7
replies
330
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
1 day ago by
sansan_96
▴ 90
2
votes
3
replies
237
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio
Cibersort
R
13 hours ago by
Azra
▴ 10
1,000 results • Page
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Recent Votes
Comment: How does gene length effect the number of reads mapped
Comment: How does gene length effect the number of reads mapped
Comment: How does gene length effect the number of reads mapped
Comment: How does gene length effect the number of reads mapped
A: Filtering of VCF, INFO DP or FORMAT DP
What is the difference between GRCh37 and hs37? And hg19?
Answer: Duplicated sequence samtools
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Recent Replies
Answer: Filtering based on alternate allelic balance
by
Arton
• 0
I found the answer when using bcftools. Is there is a way to do this with FilterVcf? bcftools filter --include '(FMT/AD[0:1])/(FMT/A…
Comment: Help with IGV abbreviation
by
GenoMax
142k
Those are SAM format fields. Check section 1.4 here: https://samtools.github.io/hts-specs/SAMv1.pdf > 1:2114:12111:13792 That is part of …
Answer: Help with IGV abbreviation
by
Mathew
▴ 120
Hi, here is a breakdown of each part that you asked about: **flag 99**: This indicates various properties of the read alignment. In this c…
Comment: Kraken2 database
by
Mathew
▴ 120
I don't see any databases with just pathogenic bacteria genomes from just a quick search, I would imagine that using the Standard-16 databa…
Comment: Galaxy StringTie error
by
Mathew
▴ 120
I am not sure if this is true for Galaxy, but when I code in Python, SyntaxWarning: invalid escape sequence '' occurs when you want to add …
Comment: Can diamond prepdb be used to make a taxonomically aware database?
by
GenoMax
142k
Should be possible: https://www.biostars.org/p/430366/ Are you using an older version of `diamond`? Latest versions of `diamond` can use N…
Comment: SNPEff database building error
by
Fungal genetics
• 0
Hi, Below SNPEff database building error I am getting. "FATAL ERROR: Most Exons do not have sequences!" The headers are correct and sam…
Comment: Extracting named fasta sequences according to list with Biopython
by
Rubayetul
• 0
the last line of SeqIO.write(record.....'fasta') in a for loop will input the the last record into new fasta file and it will only contain …
Comment: How to process Bulk WES data?
by
GenoMax
142k
You could use `sarek` (nf-core's exome pipeline) if you don't want to customize or reinvent : https://nf-co.re/sarek/3.4.2
Comment: Empty .best and .sing2 Files After Running Demuxlet
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…
Answer: FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last plac
by
David Langenberger
11k
Two last seats have just become available. Apply now, if you want them.
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr
by
GenoMax
142k
You always need to add the following option when you are using `-p` to count paired-end reads. --countReadPairs If specified, fragm…
Comment: Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so t
by
mropri
▴ 150
Hi swbarnes2, that was the problem, they were not numeric but as character columns. converted them and it fixed the error. Thank you for yo…
Answer: featureCounts output summary assigned value higher than uniquely mapped reads fr
by
Prawesh
• 0
I figured out: Since featureCounts counts fragments and not reads, we have pair-end data that means **Assigned** value from the output w…
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
by
kalavattam
▴ 190
> My question is this: "mate reverse strand" (flag 16/0x10) or "read reverse strand" (flag 32/0x20) do not directly relate to the strandedn…
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