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54 results • Page
1 of 2
Sort: replies
Rank
Views
Votes
Replies
4
votes
7
replies
377
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
10 hours ago by
Chen
• 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 13 hours ago by
Ram
43k • written 3 days ago by
ajbarrett98
• 0
4
votes
6
replies
399
views
RNA seq analysis
DESeq
RNA-seq
updated 21 hours ago by
Matthias Zepper
4.6k • written 5 days ago by
prifa
▴ 10
0
votes
5
replies
295
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
21 hours ago by
SilhouetteQ
• 0
2
votes
5
replies
173
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 7 hours ago by
Philipp Bayer
8.5k • written 10 hours ago by
林明德
• 0
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 12 hours ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 0
2
votes
4
replies
244
views
BWA alignment
Samtools
bam
updated 3 hours ago by
ATpoint
82k • written 1 day ago by
Vahid
• 0
0
votes
4
replies
119
views
Help with IGV abbreviation
Genome
browser
10 hours ago by
GeneC
• 0
0
votes
4
replies
2.2k
views
MGLTools does not work in windows 11
Autodock
MGLTools
windows
windows11
updated 8 hours ago by
Ashfaq
• 0 • written 13 months ago by
mohyeddine.taleb
• 0
1
vote
4
replies
359
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 14 hours ago by
GenoMax
142k • written 5 days ago by
Prawesh
• 0
0
votes
4
replies
157
views
Galaxy StringTie error
stringtie
galaxy
30 minutes ago by
trkfs
• 0
1
vote
4
replies
324
views
Contig assembly task, errors
dna
genetics
contig
assembly
updated 13 hours ago by
Ram
43k • written 5 days ago by
samRayne
• 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 20 hours ago by
Thind amarinder
▴ 340 • written 4.9 years ago by
garbuzov
▴ 70
3
votes
3
replies
302
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 11 hours ago by
Mathew
▴ 130 • written 3 days ago by
Christopher
• 0
1
vote
3
replies
318
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
15 hours ago by
kalavattam
▴ 190
3
votes
3
replies
250
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 13 hours ago by
Ram
43k • written 14 days ago by
Adyasha
• 0
0
votes
3
replies
250
views
Snakemake wrapper issue
fastqc
snakemake
4 hours ago by
Matvii Mykhailichenko
• 0
0
votes
3
replies
139
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 13 hours ago by
Ram
43k • written 23 hours ago by
yau
• 0
0
votes
3
replies
335
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
15 hours ago by
mropri
▴ 150
1
vote
3
replies
152
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
2 hours ago by
Vijith
▴ 30
0
votes
2
replies
63
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
1 hour ago by
IdaHao0921
• 0
1
vote
2
replies
156
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
updated 18 hours ago by
lagartija
▴ 160 • written 23 hours ago by
Esraa
• 0
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 11 hours ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 0
1
vote
2
replies
153
views
How to interpret infinite odds ratio?
statistics
32 minutes ago by
Lukas
• 0
0
votes
2
replies
376
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
14 hours ago by
David Langenberger
11k
0
votes
2
replies
24
views
How to access GWAVA software of data
GWAVA
1 hour ago by
nonaddldy
▴ 10
1
vote
2
replies
120
views
Duplicated sequence samtools
bowtie2
samtools
updated 16 hours ago by
GenoMax
142k • written 18 hours ago by
Moinuddin
• 0
1
vote
2
replies
321
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 19 hours ago by
Ram
43k • written 1 day ago by
t.fortunato.asquini
• 0
3
votes
2
replies
229
views
imputation through beagle
panel
beagle
reference
imputation
3 hours ago by
analyst
▴ 50
0
votes
1
reply
85
views
Filtering based on alternate allelic balance
GATK
Bioinformatics
Filter
VCF
10 hours ago by
Arton
• 0
0
votes
1
reply
114
views
Mouse ribosome sequences in fasta format
fasta
mm10
rRNA
updated 21 hours ago by
GenoMax
142k • written 1 day ago by
octpus616
▴ 100
0
votes
1
reply
116
views
consensus sequence calling
consensus
updated 18 hours ago by
bk11
★ 2.4k • written 22 hours ago by
Ghada
• 0
0
votes
1
reply
92
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 13 hours ago by
Ram
43k • written 15 hours ago by
eking28
• 0
0
votes
1
reply
92
views
Splitting Seurat object by sample layers
seurat
updated 13 hours ago by
Ram
43k • written 19 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 13 hours ago by
Ram
43k • written 7 days ago by
David
• 0
0
votes
1
reply
222
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 13 hours ago by
Ram
43k • written 4 days ago by
Nikki
• 0
0
votes
1
reply
106
views
How to process Bulk WES data?
WES
WGS
updated 12 hours ago by
GenoMax
142k • written 13 hours ago by
wyuan37
• 0
0
votes
1
reply
106
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 11 hours ago by
GenoMax
142k • written 14 hours ago by
cedric.blais
• 0
0
votes
1
reply
412
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
updated 23 hours ago by
aw7
▴ 280 • written 24 days ago by
abhishekghadge
• 0
0
votes
1
reply
61
views
What is the bin size for Bamcompare?
bin
chipseq
size
bamcompare
deeptools
updated 3 hours ago by
ATpoint
82k • written 7 hours ago by
Emily
▴ 20
0
votes
1
reply
82
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
updated 3 hours ago by
ATpoint
82k • written 10 hours ago by
Chen
• 0
1
vote
1
reply
92
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 3 hours ago by
zx8754
11k • written 10 hours ago by
ohtang7
▴ 40
0
votes
1
reply
71
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 2 hours ago by
ATpoint
82k • written 7 hours ago by
Pegasus
▴ 100
0
votes
1
reply
65
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
updated 2 hours ago by
Alex Reynolds
35k • written 9 hours ago by
ntsopoul
▴ 60
0
votes
0
replies
52
views
Biomart issue, why so few 3'utrs?
utr
biomart
11 hours ago by
RNAseqer
▴ 270
0
votes
0
replies
82
views
Herald:
The Biostar Herald for Monday, May 13, 2024
herald
18 hours ago by
Biostar
2.7k
0
votes
0
replies
111
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass-spectrometry
Proteins
updated 13 hours ago by
Ram
43k • written 15 days ago by
atharvakarkare14
▴ 30
0
votes
0
replies
64
views
reference-free assembly error assessment tools
assembly
17 hours ago by
lagartija
▴ 160
0
votes
0
replies
68
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
21 hours ago by
atariw
▴ 10
0
votes
0
replies
176
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
deeptools
correlation
7 hours ago by
Emily
▴ 20
54 results • Page
1 of 2
Recent Votes
A: How to get read counts on transcript level using featurecounts?
Answer: Vcf file sorting
Answer: How to interpret infinite odds ratio?
Answer: Is there any way to modify this pie chart ?
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?
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Recent Replies
Comment: Galaxy StringTie error
by
trkfs
• 0
Hi, I did not encounter any " \ - " characters in the fastq input files, and it doesn't seem to be present in any other files either. Thank…
Comment: How to interpret infinite odds ratio?
by
Lukas
• 0
Thanks you for your answer. But according that links interpretation of inf odds ratio is up to hypothesis of the researcher.So my solution …
Answer: How to access GWAVA software of data
by
nonaddldy
▴ 10
Not found in https://ftp.sanger.ac.uk/resources/software/gwava/ ![][1] [1]: /media/images/f69695ec-e047-44f6-95ce-cd4edf1c
Answer: How to access GWAVA software of data
by
nonaddldy
▴ 10
https://www.sanger.ac.uk/tool/gwava/
Comment: Is it necessary to do genotype quality filteration after snp calling with GATK
by
IdaHao0921
• 0
The species I study is not a model species, VQSR can not be applied here. I already used gatk hard-filtering. I mean, after hard-filtering,…
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
▴ 110
Hi, you can add the labels outside chart using `geom_label_repel` from `ggrepel` package. Check out this guide [https://r-charts.com/part…
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