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194 results • Page
1 of 4
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Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
just now by
IdaHao0921
• 0
0
votes
2
replies
200
views
Snakemake wrapper issue
fastqc
snakemake
updated 41 minutes ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
0
replies
14
views
What is the bin size for Bamcompare?
bin
chipseq
size
bamcompare
deeptools
1 hour ago by
Emily
▴ 20
0
votes
0
replies
28
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
1 hour ago by
Holly
• 0
0
votes
0
replies
16
views
The total expressed genes in RNA-Seq data
RNA-SEQ
2 hours ago by
Pegasus
▴ 100
2
votes
5
replies
112
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
0
votes
4
replies
2.2k
views
MGLTools does not work in windows 11
Autodock
MGLTools
windows
windows11
updated 2 hours ago by
Ashfaq
• 0 • written 13 months ago by
mohyeddine.taleb
• 0
0
votes
0
replies
30
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
4 hours ago by
ntsopoul
▴ 60
0
votes
0
replies
37
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
4 hours ago by
Chen
• 0
0
votes
0
replies
36
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
5 hours ago by
ohtang7
▴ 40
0
votes
1
reply
62
views
Filtering based on alternate allelic balance
GATK
Bioinformatics
Filter
VCF
5 hours ago by
Arton
• 0
0
votes
0
replies
34
views
Biomart issue, why so few 3'utrs?
utr
biomart
5 hours ago by
RNAseqer
▴ 270
0
votes
4
replies
87
views
Help with IGV abbreviation
Genome
browser
4 hours ago by
GeneC
• 0
0
votes
1
reply
92
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
1
reply
93
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
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
84
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
1
vote
4
replies
348
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
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
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
1
vote
2
replies
111
views
Duplicated sequence samtools
bowtie2
samtools
updated 11 hours ago by
GenoMax
142k • written 12 hours ago by
Moinuddin
• 0
0
votes
0
replies
57
views
reference-free assembly error assessment tools
assembly
12 hours ago by
lagartija
▴ 160
1
vote
2
replies
143
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
updated 12 hours ago by
lagartija
▴ 160 • written 17 hours ago by
Esraa
• 0
1
vote
0
replies
58
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
13 hours ago by
J.
▴ 10
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
1
reply
85
views
Splitting Seurat object by sample layers
seurat
updated 7 hours ago by
Ram
43k • written 14 hours ago by
kilcdincer
▴ 10
0
votes
3
replies
132
views
Galaxy StringTie error
stringtie
galaxy
updated 6 hours ago by
Mathew
▴ 130 • written 14 hours ago by
trkfs
• 0
0
votes
0
replies
61
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
16 hours ago by
atariw
▴ 10
0
votes
1
reply
107
views
Mouse ribosome sequences in fasta format
fasta
mm10
rRNA
updated 16 hours ago by
GenoMax
142k • written 1 day ago by
octpus616
▴ 100
0
votes
1
reply
93
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 16 hours ago by
Juke34
8.6k • written 17 hours ago by
Vijith
▴ 30
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
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 7 hours ago by
Ram
43k • written 18 hours ago by
yau
• 0
3
votes
2
replies
222
views
imputation through beagle
panel
beagle
reference
imputation
12 hours ago by
analyst
▴ 50
0
votes
0
replies
59
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
17 hours ago by
JACKY
▴ 140
0
votes
1
reply
381
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
updated 18 hours ago by
aw7
▴ 280 • written 24 days ago by
abhishekghadge
• 0
1
vote
1
reply
171
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
updated 18 hours ago by
aw7
▴ 280 • written 5 days ago by
Zeng Hao
▴ 40
0
votes
0
replies
71
views
Reference panel of normals for ensembl named refgenome
Mutect2
19 hours ago by
gernophil
▴ 80
1
vote
0
replies
69
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
19 hours ago by
tomas4482
▴ 400
2
votes
3
replies
211
views
BWA alignment
Samtools
bam
20 hours ago by
Vahid
• 0
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 20 hours ago by
jennyp0706
• 0
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
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
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
0
votes
1
reply
168
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
updated 1 day ago by
chrchang523
10k • written 5 days ago by
analyst
▴ 50
0
votes
0
replies
85
views
lncRNA
tcga
lncrna
1 day ago by
jain72744
▴ 10
0
votes
1
reply
212
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
updated 1 day ago by
Zhenyu Zhang
★ 1.2k • written 4 days ago by
jain72744
▴ 10
2
votes
5
replies
520
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
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
2
votes
1
reply
234
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
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
194 results • Page
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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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Recent Replies
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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