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63 results • Page
1 of 2
Sort: Votes
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Views
Votes
Replies
4
votes
7
replies
364
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
5 hours ago by
Chen
• 0
4
votes
6
replies
396
views
RNA seq analysis
DESeq
RNA-seq
updated 16 hours ago by
Matthias Zepper
4.6k • written 5 days ago by
prifa
▴ 10
3
votes
2
replies
222
views
imputation through beagle
panel
beagle
reference
imputation
12 hours ago by
analyst
▴ 50
3
votes
2
replies
140
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 20 hours ago by
ATpoint
82k • written 21 hours ago by
jennyp0706
• 0
3
votes
3
replies
296
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 6 hours ago by
Mathew
▴ 130 • written 3 days ago by
Christopher
• 0
3
votes
3
replies
248
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 7 hours ago by
Ram
43k • written 13 days ago by
Adyasha
• 0
2
votes
3
replies
241
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio
Cibersort
R
19 hours ago by
Azra
▴ 10
2
votes
4
replies
5.6k
views
44% Successfully Assigned Fragments with featureCounts after 85% uniquely mapped reads with STAR
rna-seq
alignment
RNA-Seq
featureCounts
STAR
updated 15 hours ago by
Thind amarinder
▴ 340 • written 4.9 years ago by
garbuzov
▴ 70
2
votes
3
replies
211
views
BWA alignment
Samtools
bam
21 hours ago by
Vahid
• 0
2
votes
5
replies
118
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 1 hour ago by
Philipp Bayer
8.5k • written 5 hours ago by
林明德
• 0
2
votes
13
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 23 hours ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
1
vote
2
replies
143
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
updated 13 hours ago by
lagartija
▴ 160 • written 18 hours ago by
Esraa
• 0
1
vote
0
replies
69
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
20 hours ago by
tomas4482
▴ 400
1
vote
1
reply
171
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
updated 19 hours ago by
aw7
▴ 280 • written 5 days ago by
Zeng Hao
▴ 40
1
vote
2
replies
305
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 14 hours ago by
Ram
43k • written 1 day ago by
t.fortunato.asquini
• 0
1
vote
0
replies
58
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
13 hours ago by
J.
▴ 10
1
vote
2
replies
111
views
Duplicated sequence samtools
bowtie2
samtools
updated 12 hours ago by
GenoMax
142k • written 13 hours ago by
Moinuddin
• 0
1
vote
3
replies
310
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
10 hours ago by
kalavattam
▴ 190
1
vote
4
replies
349
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 9 hours ago by
GenoMax
142k • written 5 days ago by
Prawesh
• 0
1
vote
4
replies
322
views
Contig assembly task, errors
dna
genetics
contig
assembly
updated 8 hours ago by
Ram
43k • written 5 days ago by
samRayne
• 0
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 5 hours ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 0
0
votes
1
reply
109
views
consensus sequence calling
consensus
updated 13 hours ago by
bk11
★ 2.4k • written 17 hours ago by
Ghada
• 0
0
votes
0
replies
70
views
Herald:
The Biostar Herald for Monday, May 13, 2024
herald
13 hours ago by
Biostar
2.7k
0
votes
0
replies
32
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
2 hours ago by
Holly
• 0
0
votes
0
replies
71
views
Reference panel of normals for ensembl named refgenome
Mutect2
20 hours ago by
gernophil
▴ 80
0
votes
0
replies
57
views
reference-free assembly error assessment tools
assembly
12 hours ago by
lagartija
▴ 160
0
votes
2
replies
186
views
Output file of samtools flagstat empty
samtools-flagstat
updated 20 hours ago by
colindaven
6.4k • written 1 day ago by
ramendra.sarma
• 0
0
votes
0
replies
15
views
What is the bin size for Bamcompare?
bin
chipseq
size
bamcompare
deeptools
2 hours ago by
Emily
▴ 20
0
votes
1
reply
141
views
How to interpret infinite odds ratio?
statistics
updated 11 hours ago by
bhumm
▴ 140 • written 16 hours ago by
Lukas
• 0
0
votes
0
replies
175
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
deeptools
correlation
2 hours ago by
Emily
▴ 20
0
votes
3
replies
330
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
10 hours ago by
mropri
▴ 150
0
votes
2
replies
209
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
22 hours ago by
analyst
▴ 50
0
votes
2
replies
370
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
9 hours ago by
David Langenberger
11k
0
votes
1
reply
85
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 8 hours ago by
Ram
43k • written 10 hours ago by
eking28
• 0
0
votes
1
reply
85
views
Splitting Seurat object by sample layers
seurat
updated 8 hours ago by
Ram
43k • written 14 hours ago by
kilcdincer
▴ 10
0
votes
3
replies
133
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 8 hours ago by
Ram
43k • written 18 hours ago by
yau
• 0
0
votes
6
replies
377
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 8 hours ago by
Ram
43k • written 3 days ago by
ajbarrett98
• 0
0
votes
2
replies
200
views
Snakemake wrapper issue
fastqc
snakemake
updated 51 minutes ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
0
replies
110
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass-spectrometry
Proteins
updated 7 hours ago by
Ram
43k • written 14 days ago by
atharvakarkare14
▴ 30
0
votes
1
reply
131
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence
university
assembly
protein
genomics
updated 21 hours ago by
Philipp Bayer
8.5k • written 1 day ago by
samRayne
• 0
0
votes
1
reply
135
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Cancer-Research
ATAC-seq
updated 7 hours ago by
Ram
43k • written 7 days ago by
David
• 0
0
votes
1
reply
216
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 7 hours ago by
Ram
43k • written 4 days ago by
Nikki
• 0
0
votes
1
reply
93
views
How to process Bulk WES data?
WES
WGS
updated 7 hours ago by
GenoMax
142k • written 8 hours ago by
wyuan37
• 0
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 7 hours ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 0
0
votes
1
reply
94
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 6 hours ago by
GenoMax
142k • written 9 hours ago by
cedric.blais
• 0
0
votes
3
replies
134
views
Galaxy StringTie error
stringtie
galaxy
updated 6 hours ago by
Mathew
▴ 130 • written 14 hours ago by
trkfs
• 0
0
votes
7
replies
397
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 21 hours ago by
Mohamed Abderrahmane
▴ 20 • written 14 days ago by
matteo.levorato
• 0
0
votes
0
replies
35
views
Biomart issue, why so few 3'utrs?
utr
biomart
6 hours ago by
RNAseqer
▴ 270
0
votes
0
replies
4
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
20 minutes ago by
IdaHao0921
• 0
0
votes
1
reply
64
views
Filtering based on alternate allelic balance
GATK
Bioinformatics
Filter
VCF
5 hours ago by
Arton
• 0
63 results • Page
1 of 2
Recent Votes
A: How can I convert -log10 (p-value) to p-value?
Comment: What does the 'E%' represent in BUSCO results?
Answer: What does the 'E%' represent in BUSCO results?
Answer: Combine Two Affymetrix Datasets With Same Platform
Comment: Kraken2 database
Comment: How does gene length effect the number of reads mapped
Comment: How does gene length effect the number of reads mapped
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Answer: Snakemake wrapper issue
by
Wei-Chen Pan
• 0
Hi, did you solve your problem ? I also encounter same issue but it's `wrapper:"v3.9.0/bio/picard/mergevcfs"`. In my log file, it said:…
Comment: What does the 'E%' represent in BUSCO results?
by
Philipp Bayer
8.5k
No worries! I found the commit with the maths too: https://gitlab.com/ezlab/busco/-/blame/master/src/busco/busco_tools/hmmer.py?page=2#L135…
Comment: What does the 'E%' represent in BUSCO results?
by
林明德
• 0
Thank you for your answer! It really helped me resolve a doubt!
Answer: What does the 'E%' represent in BUSCO results?
by
Philipp Bayer
8.5k
Ah your edit solved this. 50 BUSCOs contain internal stop codons, indicating they might be erroneous gene models, or the genes themselves a…
Answer: MGLTools does not work in windows 11
by
Ashfaq
• 0
In my case, I did not see iGPU. There is only one option, Intel UHD Graphics. What I need to do?
Comment: What does the 'E%' represent in BUSCO results?
by
Philipp Bayer
8.5k
funny enough i tried the same thing (i've used BUSCO heaps times but never saw the E:! even the manual lists 'C:89.0%[S:85.8%,D:3.2%],F:6.9…
Comment: What does the 'E%' represent in BUSCO results?
by
GenoMax
142k
According to ChatGPT: In BUSCO, the "E" category represents "End" or "Endof" gene fragments. These are orthologous groups for which the ge…
Comment: Help with IGV abbreviation
by
GeneC
• 0
Thank you for the link and details
Comment: Help with IGV abbreviation
by
GeneC
• 0
Thank you very much for helping with the details.
Comment: How does gene length effect the number of reads mapped
by
Chen
• 0
thank you :)
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
▴ 130
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
▴ 130
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
▴ 130
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 …
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