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1,000 results • Page
1 of 20
Sort: replies
Rank
Views
Votes
Replies
41
votes
55
replies
9.8k
views
6 follow
hash function for DNA sequences
hash
hashing
DNA
7.0 years ago by
midox
▴ 290
4
votes
45
replies
6.1k
views
SAM file wrong? help with validatesamfile
EXOME
Tutorial
updated 6.6 years ago by
Biostar
20 • written 6.8 years ago by
cristina_sabiers
▴ 110
19
votes
43
replies
4.0k
views
Annotation of huge number of CNV files
CNV annotation TCGA
4.6 years ago by
nazaninhoseinkhan
▴ 500
16
votes
38
replies
15k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 11 months ago by
Ram
38k • written 8.1 years ago by
Mo
▴ 920
17
votes
37
replies
3.2k
views
No alias or index file found for protein database
next-gen
software error
sequence
updated 3.8 years ago by
Biostar
20 • written 4.0 years ago by
williamsbrian5064
▴ 470
3
votes
32
replies
2.4k
views
fastqc report for degradome reads
fastqc
adaptor
5.0 years ago by
Sam
▴ 150
8
votes
30
replies
3.5k
views
Per Base Sequence Content
sequencing
fastqc
genome
sequence
updated 3.0 years ago by
wm
▴ 550 • written 3.0 years ago by
Negin
▴ 20
4
votes
30
replies
1.4k
views
SNPs and DEL/MNP in the same position. (DEL or SNP ??)
snp
indels
vcf
calls
mpileup
updated 2.6 years ago by
Ram
38k • written 2.6 years ago by
sami
▴ 30
4
votes
30
replies
1.3k
views
Script makes different file then the manual command, but the command is the same
pipeline
linux
awk
2.7 years ago by
stan.aanhane
▴ 30
14
votes
30
replies
2.5k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq
rna-seq
alignment
next-gen
3.9 years ago by
Malka
▴ 70
0
votes
29
replies
2.1k
views
concordance rate between SNP observed and SNP not observed
SNP
updated 4.8 years ago by
Biostar
20 • written 4.9 years ago by
nour.hadjz
▴ 20
7
votes
29
replies
1.6k
views
What's the powerful biological methods for significant genes selection?
gene selection
significant
biological method
R
4.3 years ago by
Chaimaa
▴ 260
11
votes
29
replies
8.0k
views
SummarizedExperiment nrow differs from ncol
DESeq2
SummarizedExperiment
updated 17 months ago by
Ram
38k • written 8.8 years ago by
Parham
★ 1.6k
12
votes
28
replies
1.8k
views
Calculating the expression level of genes
Gene expression
RNA-Seq
R
4.8 years ago by
Za
▴ 140
2
votes
28
replies
5.2k
views
Memory use in indexing
Assembly
software error
updated 4.6 years ago by
Ram
38k • written 4.8 years ago by
marongiu.luigi
▴ 670
9
votes
27
replies
6.0k
views
How do I use Glimmer 3.02?
sequencing
updated 4.2 years ago by
ojelizodun
• 0 • written 5.0 years ago by
nattzy94
▴ 50
3
votes
27
replies
4.6k
views
7 follow
Did anyone manage to successfully run HLAScan and get results?
HLA-Typing
NGS
updated 4.6 years ago by
Shiqi Li
• 0 • written 4.8 years ago by
zeynep
▴ 10
4
votes
27
replies
3.5k
views
MISO test run fails error of bam file was not found
RNA-Seq
Assembly
software error
next-gen
genome
updated 2.3 years ago by
Biostar
20 • written 6.6 years ago by
JoeDoasi
▴ 10
1
vote
26
replies
4.5k
views
plink --assoc command gives "NA" for all the analysis (F_A,F_U,A2,CHISQ,P,OR values)
SNP
plink
association
analysis
4.1 years ago by
kushagraprasad24
• 0
8
votes
25
replies
1.9k
views
construction of a database
sql
noSQL
neo4j
database
updated 2 days ago by
Ram
38k • written 22 months ago by
Debut
▴ 20
24
votes
25
replies
5.7k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq
beta diversity
metagenomics
2.7 years ago by
dpc
▴ 240
10
votes
25
replies
2.6k
views
The interpretation of PCA
DESeq2
R
PCA
updated 4.7 years ago by
Biostar
20 • written 4.7 years ago by
Za
▴ 140
13
votes
24
replies
3.3k
views
Error of bam-to-sam conversion using samtools
samtools
TopHat2
RNA-Seq
BAM
SAM
updated 6.0 years ago by
GenoMax
127k • written 6.0 years ago by
Gary
▴ 480
0
votes
24
replies
2.4k
views
converting spaces to tabs in gtf files
NCBI
22 months ago by
storm1907
▴ 30
5
votes
24
replies
6.8k
views
Plink1.9 gives error when converting VCF.gz to PED? "Error read failure"
VCF
Plink
4.8 years ago by
DanielC
▴ 160
11
votes
24
replies
4.0k
views
BWA mem skip orientation
assembly
genome
alignment
next-gen
3.9 years ago by
williamsbrian5064
▴ 470
1
vote
23
replies
993
views
Parse multifasta files based on a values in two columns in a metadata file
parse
mutlifasta
RefSeq
database
strain
2.6 years ago by
jmwhitha
• 0
1
vote
23
replies
1.0k
views
FASTQ exctract ID's
fastq
3.3 years ago by
User000
▴ 640
6
votes
23
replies
2.1k
views
Could you help me set up a VCF filter?
genome
software error
VCF filter
4.7 years ago by
Charlie2
▴ 50
10
votes
23
replies
1.8k
views
Two simillarly annotated sequence has no alignment similarity. Why?
blast
alignment
gene
updated 5.3 years ago by
GenoMax
127k • written 5.3 years ago by
Farbod
★ 3.4k
11
votes
22
replies
2.8k
views
No significant DEG: A request to double check my commands for limma.
limma
differential gene expression
covariates
3.9 years ago by
RNAseqer
▴ 220
23
votes
22
replies
37k
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 3 months ago by
Nicole
• 0 • written 4.9 years ago by
gaelgarcia
▴ 250
5
votes
22
replies
2.5k
views
Differential analysis between two cell lines
R
RNA-Seq
edgeR
differential analysis
4.7 years ago by
Biologist
▴ 280
0
votes
22
replies
2.5k
views
Using java Treeview to analyse genes: how to select and compile group of genes to present?
RNA-Seq
5.0 years ago by
Muha0216
• 0
1
vote
22
replies
2.4k
views
Genome Index and Alignment- STAR
RNA-Seq
genome
alignment
STAR
updated 4.3 years ago by
Kevin Blighe
84k • written 4.3 years ago by
carolgalah
• 0
5
votes
22
replies
6.4k
views
SVM for classified gene expression data
R
svm
microarray
updated 7 months ago by
Ram
38k • written 7.2 years ago by
Shaurya Jauhari
▴ 50
3
votes
22
replies
2.4k
views
Making RefSeq in Windows
refseq
6.6 years ago by
Alireza Ebadi Tabrizi
• 0
1
vote
22
replies
4.7k
views
how to use faSplit to split fasta into x files
next-gen
faSplit
sequence
4.4 years ago by
olechnwin
▴ 60
4
votes
22
replies
2.5k
views
samtools coverage usage
NGS
updated 21 months ago by
Lila M
★ 1.2k • written 21 months ago by
smrutimayipanda
▴ 20
2
votes
22
replies
1.1k
views
6 follow
Find ~1 Mb regions of genome that are shared by two or more WGS samples?
pedigree
linkage
genetics
5 months ago by
Joel Wallenius
▴ 100
13
votes
22
replies
8.8k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch effects
updated 5.5 years ago by
Biostar
20 • written 5.7 years ago by
lessismore
★ 1.3k
2
votes
21
replies
2.8k
views
Compute the correlations between submatrices
correlation
R
matrix
foreach
updated 4.0 years ago by
Ram
38k • written 4.0 years ago by
pablo
▴ 230
3
votes
21
replies
2.7k
views
Normalization agilent microarray data?
Microarray
Normalization
updated 22 months ago by
Ram
38k • written 3.5 years ago by
mathavanbioinfo
▴ 70
10
votes
21
replies
2.3k
views
Calculate disease risk based on the genoytype of some SNPs?
SNP
prs
gwas
PRSice
Plink
updated 3.6 years ago by
Biostar
20 • written 3.7 years ago by
Miguel
▴ 10
6
votes
21
replies
2.0k
views
How to evaluate the similarity of genes between two sample
RNA-Seq
differential
updated 4.5 years ago by
Biostar
20 • written 4.6 years ago by
afli
▴ 190
1
vote
21
replies
1.8k
views
Center and scale RIN values for DESeq2?
deseq2
rin
2.6 years ago by
randalljellis
▴ 90
7
votes
21
replies
2.3k
views
Merged.gtf vs. Rnor_6.0.gtf for Raw Counts
RNA-Seq
cuffmerge
raw counts
6.4 years ago by
jmsyl.hong
• 0
0
votes
21
replies
1.6k
views
HTSeq-Count: no_feature too high?
htseq-count
4 months ago by
sea.joson
▴ 10
16
votes
21
replies
1.6k
views
Why there are different hit for a same gene in different species
gene
blast
ortholog
paralog
6.5 years ago by
Farbod
★ 3.4k
5
votes
20
replies
3.2k
views
DiscoSnp Segmentation fault
snp
discosnp
updated 5 months ago by
Ram
38k • written 7.6 years ago by
Hans
▴ 130
1,000 results • Page
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Comment: bioinformatics problems solved by graphs data structure
Comment: bioinformatics problems solved by graphs data structure
Answer: How to analize multiple letters codes in COG IDs?
Answer: PCA in gene expression
Answer: PCA in gene expression
Comment: Enrichment analysis based on kegg for zebrafish
Question on number of possible alignments
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Comment: bioinformatics problems solved by graphs data structure
by
lieven.sterck
14k
et mon français est assez bien pour comprendre ce que tu as écrit la ;-)
Comment: How to analize multiple letters codes in COG IDs?
by
Constanza
• 0
Thanks for answering so fast, it was very helpful. I shouldn't pay much attention to if COGs are separated by a comma or not then. As long…
Comment: bioinformatics problems solved by graphs data structure
by
lieven.sterck
14k
well, because this is not you guys' private forum, there are other people participating (not native french speaking) , just to give a reaso…
Answer: How to get gene from PSIBLAST resuts
by
lieven.sterck
14k
what you likely will need to do: 1. get the ID of the protein that you are interested in (out of result from PSIBLAST) 2. lookup that ID…
Answer: How to analize multiple letters codes in COG IDs?
by
Mensur Dlakic
★ 23k
The meaning of individual letters is described in a well-known COG functional code: https://ecoliwiki.org/colipedia/index.php/Clusters_o…
Comment: How to find promoter sequence of a gene?
by
sunyeping
▴ 40
The organism is mice.
Answer: How to generate GFF/GTF file from cDNA transcipts FASTA file?
by
Pierre Lindenbaum
153k
BLAT your cDNAs to the reference. This should be a PSL file that can be converted to a psl->gff3 converter (e.g: https://github.com/gperte…
Comment: RNAseq: same reads + more complete scaffold = fewer DEGs?
by
Darked89
4.2k
You may try to check what happened with DEGs obtained using the 300 fragments assembly by getting the sequences of these genes and comparin…
Comment: ExomeDepth installation error
by
Medha
• 0
Thanks, that did work. Also in next steps, there are some arguments like bam.files, I was wondering do we require to have multiple bam fil…
Comment: ExomeDepth installation error
by
jared.andrews07
★ 14k
No idea, I don't use databricks. I'd read the docs, find a local expert to help you out, or contact their support, likely in that order.
Comment: ExomeDepth installation error
by
Medha
• 0
Hi @jaredandrews07 thanks for reverting back. I am new to R and just want to make sure ExomeDepth is working for the first time. For the Rs…
Comment: Embedded stop codon in translated nucleotide sequences in DAMBE
by
Mensur Dlakic
★ 23k
It is not obvious to me what exact steps you did here, but here is what I do know: there will always be stop codons even in open reading fr…
Comment: Error with a function in ATAC-seq analysis
by
Chris
▴ 70
So you skip the GRanges()? Yes, no error anymore but I am not sure if that causes changing in downstream analysis.
Answer: ClusterProfiler enrichKEGG – remove organism name in plots?
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jv
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`stringr::str_remove` can remove " - Mus musculus (house mouse)" from the pathway names which are stored under `KEGGPATHID2NAME$to` in your…
Comment: Error with a function in ATAC-seq analysis
by
jv
★ 1.0k
run `union` on the data frames
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