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396 results • Page
4 of 8
Sort: Views
Rank
Views
Votes
Replies
3
votes
4
replies
313
views
Truncated metadata file report from ENA Portal API
ena
python
5 days ago by
Giulia
• 0
0
votes
3
replies
313
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 15 days ago by
GenoMax
142k • written 16 days ago by
kim
• 0
0
votes
5
replies
311
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
2 days ago by
SilhouetteQ
• 0
0
votes
2
replies
310
views
RNAseq 1 control 2 different treatment
RNA-seq
29 days ago by
matteo.levorato
• 0
0
votes
3
replies
310
views
KEGG Pathways
r
RNA-seq
updated 15 days ago by
Ram
43k • written 15 days ago by
Sudip
• 0
0
votes
2
replies
309
views
Annovar using R package
Annovar
gnomAD
R
20 days ago by
DKA
▴ 40
0
votes
1
reply
306
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 28 days ago by
GenoMax
142k • written 28 days ago by
ycts
• 0
5
votes
5
replies
303
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
7 days ago by
Chris
▴ 280
0
votes
2
replies
303
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
28 days ago by
DKA
▴ 40
0
votes
2
replies
303
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance
Genomics
RNA-seq
Data-Analysis
updated 29 days ago by
Ram
43k • written 4 weeks ago by
David
• 0
0
votes
2
replies
303
views
Bedmethyl file format
bedmethyl
methylation
updated 28 days ago by
GenoMax
142k • written 28 days ago by
njornet
▴ 20
0
votes
1
reply
302
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 26 days ago by
GenoMax
142k • written 26 days ago by
bioyas
▴ 10
1
vote
3
replies
299
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
22 days ago by
WouterDeCoster
47k
0
votes
2
replies
298
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
28 days ago by
mropri
▴ 150
0
votes
4
replies
297
views
Correlation Analysis
statistics
methylation
NGS
expression
4 days ago by
Researcher
▴ 30
0
votes
1
reply
296
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 8 days ago by
andres.firrincieli
3.6k • written 9 days ago by
Antonio
• 0
0
votes
2
replies
294
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 3 days ago by
Zhenyu Zhang
★ 1.2k • written 12 days ago by
yahn
• 0
0
votes
4
replies
291
views
Genbank File Format
gbkformat
15 days ago by
alenew.am
• 0
0
votes
2
replies
284
views
How are score_weights calculated in this code?
single-cell
4 days ago by
carolofharvest
▴ 40
1
vote
2
replies
283
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
13 days ago by
rianna.collins
• 0
0
votes
0
replies
283
views
Choice of relatedness cutoff for GWAS of a large cohort (>100K samples)
relatedness
IBD
GWAS
updated 23 days ago by
Ram
43k • written 15 months ago by
Pine
▴ 20
1
vote
2
replies
280
views
alignment result
RNA-seq
samtools
hisat2
20 days ago by
ahmad.sajad4541
• 0
1
vote
2
replies
279
views
permutation test in edgeR
rna-seq
edgeR
updated 23 days ago by
Gordon Smyth
★ 7.2k • written 5 weeks ago by
Netanel
• 0
0
votes
2
replies
278
views
Downloading older version of a tool
Alignment
tools
11 days ago by
Ruqaiya
• 0
1
vote
3
replies
278
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 5 days ago by
Ram
43k • written 5 days ago by
Omics data mining
▴ 260
1
vote
3
replies
276
views
Odd alignment question/finding
Alignment
updated 12 days ago by
barslmn
★ 2.1k • written 13 days ago by
poordumbsillyidiot
• 0
1
vote
2
replies
273
views
Downloading full alignments from Pfam
pfam
10 days ago by
bef1
• 0
0
votes
1
reply
271
views
creating batch colum for batch correction
batch-correction
combat
9 days ago by
Expert
▴ 10
0
votes
2
replies
269
views
Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences
ANNOVAR
8 days ago by
sainavyav22
• 0
0
votes
5
replies
269
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 7 days ago by
Joe
21k • written 7 days ago by
Lemonhope
• 0
0
votes
2
replies
268
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 5 days ago by
GenoMax
142k • written 12 days ago by
Ximena
• 0
1
vote
1
reply
264
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 20 days ago by
ATpoint
82k • written 20 days ago by
AaronJaime
• 0
0
votes
1
reply
262
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 8 days ago by
GenoMax
142k • written 8 days ago by
Sony
▴ 10
3
votes
3
replies
261
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 2 days ago by
Ram
43k • written 15 days ago by
Adyasha
• 0
0
votes
0
replies
261
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
16 days ago by
SSSJec
• 0
1
vote
1
reply
255
views
Retrieve a % coverage for each transcript
RNA-seq
updated 28 days ago by
Ram
43k • written 28 days ago by
jammydodger123456
▴ 40
1
vote
3
replies
254
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 6 days ago by
GenoMax
142k • written 7 days ago by
cput
• 0
1
vote
1
reply
253
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 15 days ago by
Ram
43k • written 15 days ago by
Jonathan Yoou
▴ 60
0
votes
2
replies
252
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
8 days ago by
Ahiad Chen Zion
• 0
1
vote
3
replies
251
views
STAR aligner error
RNA-seq
STAR
slurm
updated 7 days ago by
Ram
43k • written 8 days ago by
M.
▴ 30
0
votes
1
reply
249
views
Subsetting and merging back Seurat Object brings different results
Seurat
13 days ago by
Bine
▴ 60
0
votes
4
replies
243
views
Galaxy StringTie error
stringtie
galaxy
1 day ago by
trkfs
• 0
0
votes
3
replies
242
views
Software to separate reads from different individuals
software
development
nanopore
updated 16 days ago by
GenoMax
142k • written 16 days ago by
njornet
▴ 20
2
votes
2
replies
240
views
Raw counts using stringtie
stringtie
RNA-seq
updated 12 days ago by
GenoMax
142k • written 12 days ago by
ahmad.sajad4541
• 0
1
vote
2
replies
240
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 15 days ago by
Ram
43k • written 15 days ago by
Ravita
• 0
0
votes
1
reply
238
views
Finding batch and outlayers
Pca
updated 16 days ago by
christopher medway
▴ 460 • written 17 days ago by
Tigran
• 0
2
votes
2
replies
237
views
PDB related issue
rcsb
pdb
updated 17 days ago by
noodle
▴ 580 • written 17 days ago by
Nafi
• 0
0
votes
1
reply
234
views
Help with DGEList function
DGEList
R
updated 10 days ago by
marco.barr
▴ 120 • written 11 days ago by
Natali
• 0
0
votes
0
replies
232
views
create genewise sync file in popoolation
popoolation
updated 27 days ago by
GenoMax
142k • written 27 days ago by
N.Y.Wiyana-Hewage
• 0
0
votes
2
replies
231
views
What should I consider as FASTA for dataset?
PDB
FASTA
16 days ago by
Nafi
• 0
396 results • Page
4 of 8
Recent Votes
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Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: Calculate allelic frequency from VEP output vcf file
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Comment: bbmerge (bbmap) ~ error with insert size file output
by
chrisk
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Hi Brian, Thank you and apologies for the extra future revision works. Out of curiosity we disabled neural networks 'nn=f' and the file o…
Comment: bbmerge (bbmap) ~ error with insert size file output
by
chrisk
• 0
Hi Genomax, This is the thread: https://www.biostars.org/p/9582467/ Cheers, Chris
Comment: Inquiry about deseq2 transformation
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that's helpful, thanks :)
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20k
Ah, this is a little embarrassing; those are the vectors for the neural network. I overloaded a field that was being used for the insert s…
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Thanks - I corrected it. It doesn't seem to annotate. I converted to binary after which is what is shown below. It is not the output I want…
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These are valid questions. Does your code address the concerns you've raised? From what I understand, FilterVcf is primarily designed for h…
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Found the answer here!! https://github.com/Illumina/strelka/blob/master/docs/userGuide/README.md#somatic Although this leads to a str…
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That's not a valid reason to delete the post. If that information was sensitive, posting it here was a mistake in the first place. I don't …
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Hi, regardless of how you generated the data whether with DESeq2 or other pipeline, your differential expression matrix can be used as inpu…
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Thanks. Thats work
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