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1,000 results • Page
1 of 20
Sort: replies
Rank
Views
Votes
Replies
41
votes
55
replies
12k
views
6 follow
hash function for DNA sequences
hash
hashing
DNA
8.1 years ago by
midox
▴ 290
4
votes
45
replies
7.8k
views
SAM file wrong? help with validatesamfile
EXOME
updated 13 months ago by
Ram
43k • written 7.9 years ago by
cristina_sabiers
▴ 110
19
votes
43
replies
5.6k
views
Annotation of huge number of CNV files
CNV annotation TCGA
5.7 years ago by
nazaninhoseinkhan
▴ 520
16
votes
38
replies
17k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 2.0 years ago by
Ram
43k • written 9.2 years ago by
Mo
▴ 920
17
votes
37
replies
4.8k
views
No alias or index file found for protein database
next-gen
software error
sequence
updated 4.9 years ago by
Biostar
20 • written 5.1 years ago by
williamsbrian5064
▴ 510
5
votes
35
replies
3.7k
views
Reduce set of chromosomes in Pangenome graph
pangenome
vg
updated 10 months ago by
Jordan M Eizenga
▴ 460 • written 10 months ago by
anivlete
• 0
3
votes
32
replies
3.5k
views
fastqc report for degradome reads
fastqc
adaptor
6.1 years ago by
Sam
▴ 150
8
votes
30
replies
5.2k
views
Per Base Sequence Content
sequencing
fastqc
genome
sequence
updated 4.1 years ago by
wm
▴ 560 • written 4.1 years ago by
Researcher
▴ 20
4
votes
30
replies
2.5k
views
SNPs and DEL/MNP in the same position. (DEL or SNP ??)
snp
indels
vcf
calls
mpileup
updated 3.8 years ago by
Ram
43k • written 3.8 years ago by
sami
▴ 40
14
votes
30
replies
3.4k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq
rna-seq
alignment
next-gen
5.0 years ago by
Malka
▴ 80
4
votes
30
replies
2.4k
views
Script makes different file then the manual command, but the command is the same
pipeline
linux
awk
3.8 years ago by
stan.aanhane
▴ 30
0
votes
29
replies
3.0k
views
concordance rate between SNP observed and SNP not observed
SNP
updated 5.9 years ago by
Biostar
20 • written 6.0 years ago by
nour.hadjz
▴ 20
11
votes
29
replies
9.9k
views
SummarizedExperiment nrow differs from ncol
DESeq2
SummarizedExperiment
updated 2.6 years ago by
Ram
43k • written 9.9 years ago by
Parham
★ 1.6k
7
votes
29
replies
2.5k
views
What's the powerful biological methods for significant genes selection?
gene selection
significant
biological method
R
5.4 years ago by
Chaimaa
▴ 260
2
votes
28
replies
7.6k
views
Memory use in indexing
Assembly
software error
updated 5.8 years ago by
Ram
43k • written 5.9 years ago by
marongiu.luigi
▴ 710
12
votes
28
replies
2.7k
views
Calculating the expression level of genes
Gene expression
RNA-Seq
R
5.9 years ago by
Za
▴ 140
3
votes
27
replies
5.6k
views
7 follow
Did anyone manage to successfully run HLAScan and get results?
HLA-Typing
NGS
updated 5.7 years ago by
Shiqi Li
• 0 • written 5.9 years ago by
zeynep
▴ 10
4
votes
27
replies
4.4k
views
MISO test run fails error of bam file was not found
RNA-Seq
Assembly
software error
next-gen
genome
updated 3.4 years ago by
Biostar
20 • written 7.7 years ago by
JoeDoasi
▴ 10
9
votes
27
replies
7.6k
views
How do I use Glimmer 3.02?
sequencing
updated 5.3 years ago by
ojelizodun
• 0 • written 6.1 years ago by
nattzy94
▴ 50
3
votes
26
replies
2.0k
views
6 follow
STAR Genome index Error
STAR
updated 7 months ago by
Ram
43k • written 7 months ago by
Prasanna
• 0
1
vote
26
replies
6.3k
views
plink --assoc command gives "NA" for all the analysis (F_A,F_U,A2,CHISQ,P,OR values)
SNP
plink
association
analysis
5.2 years ago by
kushagraprasad24
• 0
24
votes
25
replies
8.1k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq
beta diversity
metagenomics
3.8 years ago by
dpc
▴ 240
10
votes
25
replies
3.6k
views
The interpretation of PCA
DESeq2
R
PCA
updated 5.8 years ago by
Biostar
20 • written 5.8 years ago by
Za
▴ 140
8
votes
25
replies
3.0k
views
construction of a database
sql
noSQL
neo4j
database
updated 13 months ago by
Ram
43k • written 3.0 years ago by
Debut
▴ 20
5
votes
24
replies
8.7k
views
Plink1.9 gives error when converting VCF.gz to PED? "Error read failure"
VCF
Plink
5.9 years ago by
DanielC
▴ 170
0
votes
24
replies
3.5k
views
converting spaces to tabs in gtf files
NCBI
3.0 years ago by
storm1907
▴ 30
13
votes
24
replies
4.6k
views
Error of bam-to-sam conversion using samtools
samtools
TopHat2
RNA-Seq
BAM
SAM
updated 7.2 years ago by
GenoMax
142k • written 7.2 years ago by
Gary
▴ 480
11
votes
24
replies
5.5k
views
BWA mem skip orientation
assembly
genome
alignment
next-gen
5.0 years ago by
williamsbrian5064
▴ 510
10
votes
23
replies
2.4k
views
Two simillarly annotated sequence has no alignment similarity. Why?
blast
alignment
gene
updated 6.5 years ago by
GenoMax
142k • written 6.5 years ago by
Farbod
★ 3.4k
6
votes
23
replies
3.0k
views
Could you help me set up a VCF filter?
genome
software error
VCF filter
5.9 years ago by
Charlie2
▴ 50
1
vote
23
replies
2.1k
views
FASTQ exctract ID's
fastq
4.4 years ago by
User000
▴ 690
1
vote
23
replies
1.7k
views
Parse multifasta files based on a values in two columns in a metadata file
parse
mutlifasta
RefSeq
database
strain
3.7 years ago by
jmwhitha
• 0
11
votes
22
replies
4.2k
views
No significant DEG: A request to double check my commands for limma.
limma
differential-gene-expression
updated 28 days ago by
Ram
43k • written 5.0 years ago by
RNAseqer
▴ 270
23
votes
22
replies
50k
views
6 follow
Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KING: How do conversion tools make the PLINK .fam file, without asking …
plink
vcf
fam
gatk
vcftools
updated 17 months ago by
Nicole
• 0 • written 6.0 years ago by
gaelgarcia
▴ 260
5
votes
22
replies
7.5k
views
SVM for classified gene expression data
R
svm
microarray
updated 21 months ago by
Ram
43k • written 8.3 years ago by
Shaurya Jauhari
▴ 50
1
vote
22
replies
3.6k
views
Genome Index and Alignment- STAR
RNA-Seq
genome
alignment
STAR
updated 5.4 years ago by
Kevin Blighe
87k • written 5.4 years ago by
carolgalah
• 0
3
votes
22
replies
3.2k
views
Making RefSeq in Windows
refseq
7.8 years ago by
Alireza Ebadi Tabrizi
• 0
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch-effect
updated 21 days ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
2
votes
22
replies
2.4k
views
6 follow
Find ~1 Mb regions of genome that are shared by two or more WGS samples?
pedigree
linkage
genetics
18 months ago by
Joel Wallenius
▴ 210
0
votes
22
replies
3.4k
views
Using java Treeview to analyse genes: how to select and compile group of genes to present?
RNA-Seq
6.1 years ago by
Muha0216
• 0
5
votes
22
replies
3.3k
views
Differential analysis between two cell lines
R
RNA-Seq
edgeR
differential analysis
5.8 years ago by
Biologist
▴ 290
4
votes
22
replies
5.7k
views
samtools coverage usage
NGS
updated 2.9 years ago by
Lila M
★ 1.2k • written 2.9 years ago by
smrutimayipanda
▴ 20
1
vote
22
replies
6.2k
views
how to use faSplit to split fasta into x files
next-gen
faSplit
sequence
5.5 years ago by
olechnwin
▴ 60
2
votes
21
replies
4.2k
views
Compute the correlations between submatrices
correlation
R
matrix
foreach
updated 5.1 years ago by
Ram
43k • written 5.1 years ago by
pablo
▴ 300
16
votes
21
replies
2.3k
views
Why there are different hit for a same gene in different species
gene
blast
ortholog
paralog
7.6 years ago by
Farbod
★ 3.4k
0
votes
21
replies
2.7k
views
HTSeq-Count: no_feature too high?
htseq-count
18 months ago by
sea.joson
▴ 10
1
vote
21
replies
3.0k
views
Center and scale RIN values for DESeq2?
deseq2
rin
3.7 years ago by
randalljellis
▴ 90
7
votes
21
replies
3.2k
views
Merged.gtf vs. Rnor_6.0.gtf for Raw Counts
RNA-Seq
cuffmerge
raw counts
7.5 years ago by
jmsyl.hong
• 0
3
votes
21
replies
3.8k
views
Normalization agilent microarray data?
Microarray
Normalization
updated 3.0 years ago by
Ram
43k • written 4.6 years ago by
mathavanbioinfo
▴ 90
6
votes
21
replies
2.8k
views
How to evaluate the similarity of genes between two sample
RNA-Seq
differential
updated 5.6 years ago by
Biostar
20 • written 5.8 years ago by
afli
▴ 190
1,000 results • Page
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Comment: Phasing a mixture of two individuals' DNA with long reads
by
njornet
▴ 20
This is related to that other question but for now, the only thing I'm interested in is separating the three unique chromosomes, without as…
Comment: A question about reference genome for creating the consensus sequence
by
GenoMax
142k
> I wonder how to adjust the base genome. If you are looking to make changes to the reference you used for alignment then look into http…
Comment: Phasing a mixture of two individuals' DNA with long reads
by
GenoMax
142k
We had a related discussion in a prior thread by OP: https://www.biostars.org/p/9593780/ Do you have genotype (or independent sequence) da…
Answer: TFs and Gene databases
by
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▴ 180
I can also suggest <https://footprintdb.eead.csic.es> which links TFs to their DNA motifs, not their gene targets.
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How many methylation and expression values do you have per gene? If per gene you have a table named - *gene_corr*; which has two columns - …
Comment: How do I change the title font size in ViolinPlot (Seurat)
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★ 1.8k
thx for the explanation. I did look at the function and I also read in the help page, that you get a patchwork object, only when using `co…
Comment: Percentage coverage of reference genome by de novo genome
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Lemonhope
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Thank you, I'll check out Quast!
Answer: How do I change the title font size in ViolinPlot (Seurat)
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82k
Looking at the source code of the function it seems that they make individual plots with ggplot when `features` is `> 1` and then use patch…
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Thank you for the response to answer you question, no, the ddRADseq data (short paired end illumina reads) for all the samples were used …
Comment: Percentage coverage of reference genome by de novo genome
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54k
minimap2 can do this too, mummer (nucmer) is more accurate but slightly slower. If you want to do this as part of generating assembly stati…
Comment: TFs and Gene databases
by
ijarne
• 0
Thank you so much @jaredandrews07 it looks like I will be able to get what I intended with these sources !!
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If you have contigs for assemblies, using read-based approaches like samtools is probably not the way to go. As you're interested in % cov…
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Has data been generated in the same batch, so same day, in the same 10x runs?
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So I am assuming you have calculated a Burrows-Wheeler transform, then add the FM-index for the first and last column of the BW-matrix. I r…
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I already told them but they couldn't come up with a useful solution :/
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