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396 results • Page
4 of 8
Sort: Views
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Views
Votes
Replies
2
votes
3
replies
314
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 10 days ago by
dthorbur
★ 2.0k • written 11 days ago by
Vijith
▴ 30
1
vote
2
replies
314
views
Tumour purity and ploidy estimation
Copy-number
Whole-exome-sequencing
28 days ago by
bp22
▴ 80
1
vote
2
replies
313
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
13 days ago by
Nafi
• 0
1
vote
3
replies
312
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 13 days ago by
GenoMax
142k • written 13 days ago by
jeffrey.maurer.informatics
• 0
1
vote
2
replies
311
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
27 days ago by
bioinfo
▴ 150
0
votes
3
replies
309
views
KEGG Pathways
r
RNA-seq
updated 13 days ago by
Ram
43k • written 14 days ago by
Sudip
• 0
0
votes
3
replies
309
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 14 days ago by
GenoMax
142k • written 14 days ago by
kim
• 0
0
votes
2
replies
307
views
RNAseq 1 control 2 different treatment
RNA-seq
28 days ago by
matteo.levorato
• 0
0
votes
2
replies
307
views
Annovar using R package
Annovar
gnomAD
R
18 days ago by
DKA
▴ 40
2
votes
2
replies
306
views
How to row normalize a matrixplot?
scRNA-seq
RNA-seq
single-cell
scanpy
28 days ago by
bioinfo
▴ 150
0
votes
1
reply
305
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 26 days ago by
GenoMax
142k • written 26 days ago by
ycts
• 0
0
votes
2
replies
302
views
Bedmethyl file format
bedmethyl
methylation
updated 27 days ago by
GenoMax
142k • written 27 days ago by
njornet
▴ 20
0
votes
2
replies
301
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance
Genomics
RNA-seq
Data-Analysis
updated 27 days ago by
Ram
43k • written 28 days ago by
David
• 0
3
votes
4
replies
300
views
Truncated metadata file report from ENA Portal API
ena
python
3 days ago by
Giulia
• 0
0
votes
2
replies
296
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
27 days ago by
DKA
▴ 40
0
votes
2
replies
296
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
27 days ago by
mropri
▴ 150
0
votes
1
reply
296
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 24 days ago by
GenoMax
142k • written 24 days ago by
bioyas
▴ 10
0
votes
5
replies
295
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
23 hours ago by
SilhouetteQ
• 0
1
vote
3
replies
291
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
21 days ago by
WouterDeCoster
47k
5
votes
5
replies
291
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
6 days ago by
Chris
▴ 280
0
votes
1
reply
291
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 7 days ago by
andres.firrincieli
3.6k • written 8 days ago by
Antonio
• 0
0
votes
4
replies
289
views
Genbank File Format
gbkformat
14 days ago by
alenew.am
• 0
0
votes
2
replies
288
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 1 day ago by
Zhenyu Zhang
★ 1.2k • written 10 days ago by
yahn
• 0
0
votes
0
replies
283
views
Choice of relatedness cutoff for GWAS of a large cohort (>100K samples)
relatedness
IBD
GWAS
updated 21 days ago by
Ram
43k • written 14 months ago by
Pine
▴ 20
0
votes
4
replies
282
views
Correlation Analysis
statistics
methylation
NGS
expression
3 days ago by
Researcher
▴ 30
0
votes
1
reply
281
views
Two databases: Human Microbiome Project and MGnify
Microbiome
databases
updated 28 days ago by
GenoMax
142k • written 28 days ago by
haiying.kong
▴ 360
1
vote
2
replies
280
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
12 days ago by
rianna.collins
• 0
1
vote
2
replies
276
views
alignment result
RNA-seq
samtools
hisat2
19 days ago by
ahmad.sajad4541
• 0
1
vote
2
replies
274
views
permutation test in edgeR
rna-seq
edgeR
updated 22 days ago by
Gordon Smyth
★ 7.2k • written 5 weeks ago by
Netanel
• 0
0
votes
2
replies
272
views
Downloading older version of a tool
Alignment
tools
10 days ago by
Ruqaiya
• 0
0
votes
1
reply
269
views
creating batch colum for batch correction
batch-correction
combat
8 days ago by
Expert
▴ 10
0
votes
2
replies
268
views
How are score_weights calculated in this code?
single-cell
3 days ago by
carolofharvest
▴ 40
1
vote
3
replies
267
views
Odd alignment question/finding
Alignment
updated 11 days ago by
barslmn
★ 2.1k • written 12 days ago by
poordumbsillyidiot
• 0
1
vote
3
replies
267
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 3 days ago by
Ram
43k • written 3 days ago by
Omics data mining
▴ 260
1
vote
2
replies
263
views
Downloading full alignments from Pfam
pfam
8 days ago by
bef1
• 0
0
votes
2
replies
262
views
Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences
ANNOVAR
6 days ago by
sainavyav22
• 0
1
vote
1
reply
260
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 18 days ago by
ATpoint
82k • written 18 days ago by
AaronJaime
• 0
0
votes
2
replies
260
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 3 days ago by
GenoMax
142k • written 10 days ago by
Ximena
• 0
0
votes
0
replies
256
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
14 days ago by
SSSJec
• 0
1
vote
1
reply
255
views
Retrieve a % coverage for each transcript
RNA-seq
updated 26 days ago by
Ram
43k • written 26 days ago by
jammydodger123456
▴ 40
0
votes
5
replies
255
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 6 days ago by
Joe
21k • written 6 days ago by
Lemonhope
• 0
0
votes
1
reply
252
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 6 days ago by
GenoMax
142k • written 6 days ago by
Sony
▴ 10
3
votes
3
replies
252
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 14 hours ago by
Ram
43k • written 14 days ago by
Adyasha
• 0
1
vote
1
reply
250
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 13 days ago by
Ram
43k • written 13 days ago by
Jonathan Yoou
▴ 60
0
votes
1
reply
245
views
merging Seurat objects after SCT
Seurat
SCT
updated 28 days ago by
Ram
43k • written 28 days ago by
michelle.swarovski
• 0
0
votes
2
replies
245
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
6 days ago by
Ahiad Chen Zion
• 0
0
votes
1
reply
244
views
Subsetting and merging back Seurat Object brings different results
Seurat
11 days ago by
Bine
▴ 60
1
vote
3
replies
243
views
STAR aligner error
RNA-seq
STAR
slurm
updated 5 days ago by
Ram
43k • written 6 days ago by
M.
▴ 30
1
vote
3
replies
242
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 4 days ago by
GenoMax
142k • written 5 days ago by
cput
• 0
0
votes
3
replies
241
views
Software to separate reads from different individuals
software
development
nanopore
updated 14 days ago by
GenoMax
142k • written 14 days ago by
njornet
▴ 20
396 results • Page
4 of 8
Recent Votes
Comment: Help with IGV abbreviation
A: How to get read counts on transcript level using featurecounts?
Answer: Vcf file sorting
Answer: How to interpret infinite odds ratio?
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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?
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Comment: CNVKIT - unable to produce scatter and diagram pdfs
by
Anitha
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The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
Answer: CNVkit for somatic copy number detection
by
Anitha
• 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
Comment: CNVkit for somatic copy number detection
by
Anitha
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The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
Answer: Overlapping Ranges within Granges object
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There is no one-hit function in GenomicRanges, but you can stick something together using a combination of `findOverlaps` to first find ove…
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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
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https://www.sanger.ac.uk/tool/gwava/
Comment: Is it necessary to do genotype quality filteration after snp calling with GATK
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• 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
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▴ 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…
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I have tried installing AGAT. But it failed the tests. …
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82k
That is not what the logs above tell, but good you solved it.
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The transformations first correct for sequencing depth (and [composition][1]) and then apply the variance stabilization / regularization. N…
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There is no robust definition of "expressed" genes, this has been asked many times before. edgeR doesn't care about "expressed", it cares (…
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