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1,000 results • Page
1 of 20
Sort: replies
Rank
Views
Votes
Replies
41
votes
55
replies
10k
views
6 follow
hash function for DNA sequences
hash
hashing
DNA
7.2 years ago by
midox
▴ 290
4
votes
45
replies
6.3k
views
SAM file wrong? help with validatesamfile
EXOME
updated 8 weeks ago by
Ram
39k • written 7.0 years ago by
cristina_sabiers
▴ 110
19
votes
43
replies
4.2k
views
Annotation of huge number of CNV files
CNV annotation TCGA
4.8 years ago by
nazaninhoseinkhan
▴ 510
16
votes
38
replies
16k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 13 months ago by
Ram
39k • written 8.3 years ago by
Mo
▴ 920
17
votes
37
replies
3.5k
views
No alias or index file found for protein database
next-gen
software error
sequence
updated 4.0 years ago by
Biostar
20 • written 4.2 years ago by
williamsbrian5064
▴ 470
3
votes
32
replies
2.6k
views
fastqc report for degradome reads
fastqc
adaptor
5.2 years ago by
Sam
▴ 150
4
votes
30
replies
1.6k
views
SNPs and DEL/MNP in the same position. (DEL or SNP ??)
snp
indels
vcf
calls
mpileup
updated 2.9 years ago by
Ram
39k • written 2.9 years ago by
sami
▴ 30
8
votes
30
replies
3.9k
views
Per Base Sequence Content
sequencing
fastqc
genome
sequence
updated 3.2 years ago by
wm
▴ 550 • written 3.2 years ago by
Negin
▴ 20
4
votes
30
replies
1.4k
views
Script makes different file then the manual command, but the command is the same
pipeline
linux
awk
2.9 years ago by
stan.aanhane
▴ 30
14
votes
30
replies
2.6k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq
rna-seq
alignment
next-gen
4.1 years ago by
Malka
▴ 70
0
votes
29
replies
2.2k
views
concordance rate between SNP observed and SNP not observed
SNP
updated 5.0 years ago by
Biostar
20 • written 5.1 years ago by
nour.hadjz
▴ 20
11
votes
29
replies
8.3k
views
SummarizedExperiment nrow differs from ncol
DESeq2
SummarizedExperiment
updated 20 months ago by
Ram
39k • written 9.0 years ago by
Parham
★ 1.6k
7
votes
29
replies
1.7k
views
What's the powerful biological methods for significant genes selection?
gene selection
significant
biological method
R
4.5 years ago by
Chaimaa
▴ 260
12
votes
28
replies
1.9k
views
Calculating the expression level of genes
Gene expression
RNA-Seq
R
5.0 years ago by
Za
▴ 140
2
votes
28
replies
5.6k
views
Memory use in indexing
Assembly
software error
updated 4.8 years ago by
Ram
39k • written 5.0 years ago by
marongiu.luigi
▴ 680
9
votes
27
replies
6.3k
views
How do I use Glimmer 3.02?
sequencing
updated 4.4 years ago by
ojelizodun
• 0 • written 5.2 years ago by
nattzy94
▴ 50
4
votes
27
replies
3.7k
views
MISO test run fails error of bam file was not found
RNA-Seq
Assembly
software error
next-gen
genome
updated 2.5 years ago by
Biostar
20 • written 6.8 years ago by
JoeDoasi
▴ 10
3
votes
27
replies
4.8k
views
7 follow
Did anyone manage to successfully run HLAScan and get results?
HLA-Typing
NGS
updated 4.8 years ago by
Shiqi Li
• 0 • written 5.0 years ago by
zeynep
▴ 10
1
vote
26
replies
4.9k
views
plink --assoc command gives "NA" for all the analysis (F_A,F_U,A2,CHISQ,P,OR values)
SNP
plink
association
analysis
4.3 years ago by
kushagraprasad24
• 0
24
votes
25
replies
6.2k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq
beta diversity
metagenomics
2.9 years ago by
dpc
▴ 240
8
votes
25
replies
2.1k
views
construction of a database
sql
noSQL
neo4j
database
updated 11 weeks ago by
Ram
39k • written 2.0 years ago by
Debut
▴ 20
10
votes
25
replies
2.7k
views
The interpretation of PCA
DESeq2
R
PCA
updated 4.9 years ago by
Biostar
20 • written 4.9 years ago by
Za
▴ 140
0
votes
24
replies
2.7k
views
converting spaces to tabs in gtf files
NCBI
2.1 years ago by
storm1907
▴ 30
5
votes
24
replies
7.2k
views
Plink1.9 gives error when converting VCF.gz to PED? "Error read failure"
VCF
Plink
5.0 years ago by
DanielC
▴ 160
11
votes
24
replies
4.2k
views
BWA mem skip orientation
assembly
genome
alignment
next-gen
4.1 years ago by
williamsbrian5064
▴ 470
13
votes
24
replies
3.5k
views
Error of bam-to-sam conversion using samtools
samtools
TopHat2
RNA-Seq
BAM
SAM
updated 6.2 years ago by
GenoMax
130k • written 6.2 years ago by
Gary
▴ 480
1
vote
23
replies
1.2k
views
FASTQ exctract ID's
fastq
3.5 years ago by
User000
▴ 660
10
votes
23
replies
1.8k
views
Two simillarly annotated sequence has no alignment similarity. Why?
blast
alignment
gene
updated 5.6 years ago by
GenoMax
130k • written 5.6 years ago by
Farbod
★ 3.4k
1
vote
23
replies
1.1k
views
Parse multifasta files based on a values in two columns in a metadata file
parse
mutlifasta
RefSeq
database
strain
2.8 years ago by
jmwhitha
• 0
6
votes
23
replies
2.2k
views
Could you help me set up a VCF filter?
genome
software error
VCF filter
4.9 years ago by
Charlie2
▴ 50
11
votes
22
replies
3.0k
views
No significant DEG: A request to double check my commands for limma.
limma
differential gene expression
covariates
4.1 years ago by
RNAseqer
▴ 240
23
votes
22
replies
40k
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 6 months ago by
Nicole
• 0 • written 5.1 years ago by
gaelgarcia
▴ 250
5
votes
22
replies
2.6k
views
Differential analysis between two cell lines
R
RNA-Seq
edgeR
differential analysis
4.9 years ago by
Biologist
▴ 280
0
votes
22
replies
2.7k
views
Using java Treeview to analyse genes: how to select and compile group of genes to present?
RNA-Seq
5.2 years ago by
Muha0216
• 0
1
vote
22
replies
2.6k
views
Genome Index and Alignment- STAR
RNA-Seq
genome
alignment
STAR
updated 4.5 years ago by
Kevin Blighe
85k • written 4.5 years ago by
carolgalah
• 0
3
votes
22
replies
2.5k
views
Making RefSeq in Windows
refseq
6.9 years ago by
Alireza Ebadi Tabrizi
• 0
5
votes
22
replies
6.6k
views
SVM for classified gene expression data
R
svm
microarray
updated 10 months ago by
Ram
39k • written 7.4 years ago by
Shaurya Jauhari
▴ 50
1
vote
22
replies
5.0k
views
how to use faSplit to split fasta into x files
next-gen
faSplit
sequence
4.6 years ago by
olechnwin
▴ 60
2
votes
22
replies
1.3k
views
6 follow
Find ~1 Mb regions of genome that are shared by two or more WGS samples?
pedigree
linkage
genetics
7 months ago by
Joel Wallenius
▴ 130
4
votes
22
replies
2.9k
views
samtools coverage usage
NGS
updated 23 months ago by
Lila M
★ 1.2k • written 23 months ago by
smrutimayipanda
▴ 20
13
votes
22
replies
9.2k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch effects
updated 5.7 years ago by
Biostar
20 • written 5.9 years ago by
lessismore
★ 1.3k
2
votes
21
replies
3.0k
views
Compute the correlations between submatrices
correlation
R
matrix
foreach
updated 4.2 years ago by
Ram
39k • written 4.2 years ago by
pablo
▴ 250
16
votes
21
replies
1.6k
views
Why there are different hit for a same gene in different species
gene
blast
ortholog
paralog
6.7 years ago by
Farbod
★ 3.4k
3
votes
21
replies
3.0k
views
Normalization agilent microarray data?
Microarray
Normalization
updated 2.1 years ago by
Ram
39k • written 3.7 years ago by
mathavanbioinfo
▴ 70
6
votes
21
replies
2.1k
views
How to evaluate the similarity of genes between two sample
RNA-Seq
differential
updated 4.7 years ago by
Biostar
20 • written 4.8 years ago by
afli
▴ 190
1
vote
21
replies
2.0k
views
Center and scale RIN values for DESeq2?
deseq2
rin
2.8 years ago by
randalljellis
▴ 90
10
votes
21
replies
2.4k
views
Calculate disease risk based on the genoytype of some SNPs?
SNP
prs
gwas
PRSice
Plink
updated 3.8 years ago by
Biostar
20 • written 3.9 years ago by
Miguel
▴ 10
7
votes
21
replies
2.4k
views
Merged.gtf vs. Rnor_6.0.gtf for Raw Counts
RNA-Seq
cuffmerge
raw counts
6.6 years ago by
jmsyl.hong
• 0
0
votes
21
replies
1.8k
views
HTSeq-Count: no_feature too high?
htseq-count
7 months ago by
sea.joson
▴ 10
22
votes
20
replies
2.1k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
blast
RNA-Seq
genome
gene
updated 8 weeks ago by
Ram
39k • written 6.9 years ago by
Farbod
★ 3.4k
1,000 results • Page
1 of 20
Recent Votes
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
A: Mouse promoter regions
Answer: How to get information about promoter from bulk-RNAseq?
A: Extracting Flanking Regions across TSS using R scripts
A: Mouse promoter regions
A: Finding zebrafish promoters ENSEMBL
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Comment: How to get information about promoter from bulk-RNAseq?
by
camillab.
▴ 130
and what about enhancer? is it possible to do it from a bulk-RNAseq?
Comment: How to get information about promoter from bulk-RNAseq?
by
camillab.
▴ 130
yes! clearly the terminology on my side needs to improved!
Comment: How to get information about promoter from bulk-RNAseq?
by
rpolicastro
12k
Generally speaking, most promoters only initiate transcription for a single gene, with a single gene potentially having multiple promoters …
Answer: How to get information about promoter from bulk-RNAseq?
by
Trivas
★ 1.2k
I'd probably select the genes of interest from your bulk RNA-seq results then use the UCSC table browser to get the sequence upstream of th…
Comment: How to add annotation columns with specific colors to the heatmap?
by
Ram
39k
Show us your exact code - it is quite easy to tweak colors in ComplexHeatmap with the `col=` argument.
Comment: VCF file CSQ flag
by
Ram
39k
True, but it's not technically impossible to annotate GVCFs, which is why I did not address that point.
Comment: Creating a local version of Clustered NR database
by
PeterC_NCBI
▴ 260
@genomax Sorry for the delay in reply. We're still working out the details of what exactly to provide. One idea is to provide just the rep…
Comment: Shannon's Entropy by Sliding Window in R
by
rohitsatyam102
▴ 690
Hi Were u able to achieve this?
Comment: Differences in GTF files hg19 and hg38
by
GenoMax
130k
Since this is not an answer to the original question do not add it as such. I moved your last comment to the correct spot it should have be…
Comment: VCF file CSQ flag
by
Pierre Lindenbaum
154k
if your talking about the gvcf produced by HaplotypeCaller with ERC=GVCF, you don't annote g.vcf files , you must first merge the g.vcf.f…
Comment: [python]sklearn.ensemble.RandomForestClassifier(TypeError: string indices must b
by
Ram
39k
https://www.biostars.org/u/127538/ : Please delete this question or it will be deleted by moderators in a few days.
Comment: VCF file CSQ flag
by
Ram
39k
A gvcf files has blocks for both variant loci and non-variant loci, so you won't see a CSQ for each record, only for those variant loci wit…
Comment: Differences in GTF files hg19 and hg38
by
heureuse
• 0
Thank you very much. I get it from UCSC.
Comment: [python]sklearn.ensemble.RandomForestClassifier(TypeError: string indices must b
by
Arup Ghosh
3.2k
This post does not fit the theme of this forum.
Comment: CellRanger problem
by
Arup Ghosh
3.2k
Try with atleast 32 GB of Memory rather than 16 GB specified by `limitGenomeGenerateRAM` option.
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