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59 results • Page
1 of 2
Sort: replies
Rank
Views
Votes
Replies
4
votes
7
replies
371
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
8 hours ago by
Chen
• 0
4
votes
6
replies
398
views
RNA seq analysis
DESeq
RNA-seq
updated 19 hours ago by
Matthias Zepper
4.6k • written 5 days ago by
prifa
▴ 10
0
votes
6
replies
377
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 11 hours ago by
Ram
43k • written 3 days ago by
ajbarrett98
• 0
0
votes
5
replies
295
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
19 hours ago by
SilhouetteQ
• 0
2
votes
5
replies
158
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 5 hours ago by
Philipp Bayer
8.5k • written 8 hours ago by
林明德
• 0
1
vote
4
replies
323
views
Contig assembly task, errors
dna
genetics
contig
assembly
updated 11 hours ago by
Ram
43k • written 5 days ago by
samRayne
• 0
0
votes
4
replies
112
views
Help with IGV abbreviation
Genome
browser
8 hours ago by
GeneC
• 0
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 10 hours ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 0
2
votes
4
replies
228
views
BWA alignment
Samtools
bam
updated 1 hour ago by
ATpoint
82k • written 1 day ago by
Vahid
• 0
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 18 hours ago by
Thind amarinder
▴ 340 • written 4.9 years ago by
garbuzov
▴ 70
0
votes
4
replies
2.2k
views
MGLTools does not work in windows 11
Autodock
MGLTools
windows
windows11
updated 6 hours ago by
Ashfaq
• 0 • written 13 months ago by
mohyeddine.taleb
• 0
1
vote
4
replies
353
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 12 hours ago by
GenoMax
142k • written 5 days ago by
Prawesh
• 0
1
vote
3
replies
313
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
13 hours ago by
kalavattam
▴ 190
0
votes
3
replies
332
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
13 hours ago by
mropri
▴ 150
3
votes
3
replies
248
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 10 hours ago by
Ram
43k • written 14 days ago by
Adyasha
• 0
2
votes
3
replies
242
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio
Cibersort
R
22 hours ago by
Azra
▴ 10
0
votes
3
replies
136
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 11 hours ago by
Ram
43k • written 21 hours ago by
yau
• 0
3
votes
3
replies
301
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 9 hours ago by
Mathew
▴ 130 • written 3 days ago by
Christopher
• 0
0
votes
3
replies
146
views
Galaxy StringTie error
stringtie
galaxy
updated 9 hours ago by
Mathew
▴ 130 • written 17 hours ago by
trkfs
• 0
0
votes
3
replies
239
views
Snakemake wrapper issue
fastqc
snakemake
2 hours ago by
Matvii Mykhailichenko
• 0
1
vote
3
replies
124
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
47 minutes ago by
Vijith
▴ 30
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 8 hours ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 0
1
vote
2
replies
315
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 17 hours ago by
Ram
43k • written 1 day ago by
t.fortunato.asquini
• 0
1
vote
2
replies
153
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
updated 16 hours ago by
lagartija
▴ 160 • written 21 hours ago by
Esraa
• 0
1
vote
2
replies
115
views
Duplicated sequence samtools
bowtie2
samtools
updated 15 hours ago by
GenoMax
142k • written 16 hours ago by
Moinuddin
• 0
3
votes
2
replies
147
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 23 hours ago by
ATpoint
82k • written 1 day ago by
jennyp0706
• 0
0
votes
2
replies
373
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
12 hours ago by
David Langenberger
11k
0
votes
2
replies
187
views
Output file of samtools flagstat empty
samtools-flagstat
updated 23 hours ago by
colindaven
6.4k • written 1 day ago by
ramendra.sarma
• 0
3
votes
2
replies
226
views
imputation through beagle
panel
beagle
reference
imputation
1 hour ago by
analyst
▴ 50
0
votes
1
reply
48
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
updated 10 minutes ago by
Alex Reynolds
35k • written 7 hours ago by
ntsopoul
▴ 60
1
vote
1
reply
175
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
updated 22 hours ago by
aw7
▴ 280 • written 5 days ago by
Zeng Hao
▴ 40
0
votes
1
reply
390
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
updated 21 hours ago by
aw7
▴ 280 • written 24 days ago by
abhishekghadge
• 0
0
votes
1
reply
110
views
Mouse ribosome sequences in fasta format
fasta
mm10
rRNA
updated 19 hours ago by
GenoMax
142k • written 1 day ago by
octpus616
▴ 100
0
votes
1
reply
112
views
consensus sequence calling
consensus
updated 16 hours ago by
bk11
★ 2.4k • written 20 hours ago by
Ghada
• 0
0
votes
1
reply
144
views
How to interpret infinite odds ratio?
statistics
updated 14 hours ago by
bhumm
▴ 140 • written 19 hours ago by
Lukas
• 0
0
votes
1
reply
88
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 11 hours ago by
Ram
43k • written 13 hours ago by
eking28
• 0
0
votes
1
reply
88
views
Splitting Seurat object by sample layers
seurat
updated 11 hours ago by
Ram
43k • written 17 hours ago by
kilcdincer
▴ 10
0
votes
1
reply
136
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Cancer-Research
ATAC-seq
updated 10 hours ago by
Ram
43k • written 7 days ago by
David
• 0
0
votes
1
reply
219
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 10 hours ago by
Ram
43k • written 4 days ago by
Nikki
• 0
0
votes
1
reply
99
views
How to process Bulk WES data?
WES
WGS
updated 10 hours ago by
GenoMax
142k • written 11 hours ago by
wyuan37
• 0
0
votes
1
reply
103
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 9 hours ago by
GenoMax
142k • written 12 hours ago by
cedric.blais
• 0
0
votes
1
reply
80
views
Filtering based on alternate allelic balance
GATK
Bioinformatics
Filter
VCF
8 hours ago by
Arton
• 0
0
votes
1
reply
35
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
updated 1 hour ago by
Pierre Lindenbaum
161k • written 3 hours ago by
IdaHao0921
• 0
0
votes
1
reply
44
views
What is the bin size for Bamcompare?
bin
chipseq
size
bamcompare
deeptools
updated 1 hour ago by
ATpoint
82k • written 5 hours ago by
Emily
▴ 20
0
votes
1
reply
66
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
updated 1 hour ago by
ATpoint
82k • written 8 hours ago by
Chen
• 0
1
vote
1
reply
80
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 1 hour ago by
zx8754
11k • written 8 hours ago by
ohtang7
▴ 40
0
votes
1
reply
55
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 22 minutes ago by
ATpoint
82k • written 5 hours ago by
Pegasus
▴ 100
1
vote
0
replies
63
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
16 hours ago by
J.
▴ 10
0
votes
0
replies
25
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
2 hours ago by
Spring
• 0
0
votes
0
replies
77
views
Herald:
The Biostar Herald for Monday, May 13, 2024
herald
16 hours ago by
Biostar
2.7k
59 results • Page
1 of 2
Recent Votes
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
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
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Recent Replies
Answer: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
If you're not tied to Granges, you could use `bedmap --fraction-both 0.1` to require at least 10% overlap between reference and map regions…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
by
Vijith
▴ 30
By doing some online search, I tried installing one module `cpan Bio::DB::Fasta` and it is running like a never-ending installation process…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
by
Vijith
▴ 30
I have tried installing AGAT. But it failed the tests. …
Comment: BWA alignment
by
ATpoint
82k
That is not what the logs above tell, but good you solved it.
Answer: Inquiry about deseq2 transformation
by
ATpoint
82k
The transformations first correct for sequencing depth (and [composition][1]) and then apply the variance stabilization / regularization. N…
Answer: The total expressed genes in RNA-Seq data
by
ATpoint
82k
There is no robust definition of "expressed" genes, this has been asked many times before. edgeR doesn't care about "expressed", it cares (…
Answer: What is the bin size for Bamcompare?
by
ATpoint
82k
It is the number of adjacent bases that are aggregated (binned) into a single value. I find binning not optimal, and would always set this …
Comment: Is it necessary to do genotype quality filteration after snp calling with GATK
by
Pierre Lindenbaum
161k
see VQSR https://gatk.broadinstitute.org/hc/en-us/articles/360035531612-Variant-Quality-Score-Recalibration-VQSR and https://gatk.broadinst…
Comment: Snakemake wrapper issue
by
Matvii Mykhailichenko
• 0
Hi, I kind of did and kind of didn't: I stopped trying to use snakemake( I remember that it's a lot of hustle to install pickard, maybe you…
Answer: Is there any way to modify this pie chart ?
by
marco.barr
▴ 100
Hi, you can add the labels outside chart using `geom_label_repel` from `ggrepel` package. Check out this guide [https://r-charts.com/part…
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?
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