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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
8.0 years ago by
midox
▴ 290
4
votes
45
replies
7.5k
views
SAM file wrong? help with validatesamfile
EXOME
updated 11 months ago by
Ram
43k • written 7.8 years ago by
cristina_sabiers
▴ 110
19
votes
43
replies
5.5k
views
Annotation of huge number of CNV files
CNV annotation TCGA
5.6 years ago by
nazaninhoseinkhan
▴ 520
16
votes
38
replies
17k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 23 months ago by
Ram
43k • written 9.1 years ago by
Mo
▴ 920
17
votes
37
replies
4.6k
views
No alias or index file found for protein database
next-gen
software error
sequence
updated 4.8 years ago by
Biostar
20 • written 5.0 years ago by
williamsbrian5064
▴ 510
5
votes
35
replies
3.5k
views
Reduce set of chromosomes in Pangenome graph
pangenome
vg
updated 8 months ago by
Jordan M Eizenga
▴ 460 • written 9 months ago by
anivlete
• 0
3
votes
32
replies
3.3k
views
fastqc report for degradome reads
fastqc
adaptor
6.0 years ago by
Sam
▴ 150
8
votes
30
replies
5.0k
views
Per Base Sequence Content
sequencing
fastqc
genome
sequence
updated 4.0 years ago by
wm
▴ 550 • written 4.0 years ago by
Researcher
▴ 20
4
votes
30
replies
2.3k
views
Script makes different file then the manual command, but the command is the same
pipeline
linux
awk
3.7 years ago by
stan.aanhane
▴ 30
14
votes
30
replies
3.3k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq
rna-seq
alignment
next-gen
4.9 years ago by
Malka
▴ 80
4
votes
30
replies
2.3k
views
SNPs and DEL/MNP in the same position. (DEL or SNP ??)
snp
indels
vcf
calls
mpileup
updated 3.7 years ago by
Ram
43k • written 3.7 years ago by
sami
▴ 30
0
votes
29
replies
2.8k
views
concordance rate between SNP observed and SNP not observed
SNP
updated 5.8 years ago by
Biostar
20 • written 5.9 years ago by
nour.hadjz
▴ 20
11
votes
29
replies
9.6k
views
SummarizedExperiment nrow differs from ncol
DESeq2
SummarizedExperiment
updated 2.4 years ago by
Ram
43k • written 9.8 years ago by
Parham
★ 1.6k
7
votes
29
replies
2.4k
views
What's the powerful biological methods for significant genes selection?
gene selection
significant
biological method
R
5.3 years ago by
Chaimaa
▴ 260
12
votes
28
replies
2.6k
views
Calculating the expression level of genes
Gene expression
RNA-Seq
R
5.8 years ago by
Za
▴ 140
2
votes
28
replies
7.3k
views
Memory use in indexing
Assembly
software error
updated 5.6 years ago by
Ram
43k • written 5.8 years ago by
marongiu.luigi
▴ 710
3
votes
27
replies
5.5k
views
7 follow
Did anyone manage to successfully run HLAScan and get results?
HLA-Typing
NGS
updated 5.6 years ago by
Shiqi Li
• 0 • written 5.8 years ago by
zeynep
▴ 10
9
votes
27
replies
7.4k
views
How do I use Glimmer 3.02?
sequencing
updated 5.2 years ago by
ojelizodun
• 0 • written 6.0 years ago by
nattzy94
▴ 50
4
votes
27
replies
4.2k
views
MISO test run fails error of bam file was not found
RNA-Seq
Assembly
software error
next-gen
genome
updated 3.3 years ago by
Biostar
20 • written 7.6 years ago by
JoeDoasi
▴ 10
1
vote
26
replies
6.0k
views
plink --assoc command gives "NA" for all the analysis (F_A,F_U,A2,CHISQ,P,OR values)
SNP
plink
association
analysis
5.1 years ago by
kushagraprasad24
• 0
3
votes
26
replies
1.8k
views
6 follow
STAR Genome index Error
STAR
updated 5 months ago by
Ram
43k • written 5 months ago by
Prasanna
• 0
8
votes
25
replies
2.9k
views
construction of a database
sql
noSQL
neo4j
database
updated 12 months ago by
Ram
43k • written 2.9 years ago by
Debut
▴ 20
10
votes
25
replies
3.4k
views
The interpretation of PCA
DESeq2
R
PCA
updated 5.7 years ago by
Biostar
20 • written 5.7 years ago by
Za
▴ 140
24
votes
25
replies
7.9k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq
beta diversity
metagenomics
3.7 years ago by
dpc
▴ 240
5
votes
24
replies
8.6k
views
Plink1.9 gives error when converting VCF.gz to PED? "Error read failure"
VCF
Plink
5.8 years ago by
DanielC
▴ 160
11
votes
24
replies
5.3k
views
BWA mem skip orientation
assembly
genome
alignment
next-gen
4.9 years ago by
williamsbrian5064
▴ 510
0
votes
24
replies
3.4k
views
converting spaces to tabs in gtf files
NCBI
2.9 years ago by
storm1907
▴ 30
13
votes
24
replies
4.4k
views
Error of bam-to-sam conversion using samtools
samtools
TopHat2
RNA-Seq
BAM
SAM
updated 7.1 years ago by
GenoMax
140k • written 7.1 years ago by
Gary
▴ 480
10
votes
23
replies
2.4k
views
Two simillarly annotated sequence has no alignment similarity. Why?
blast
alignment
gene
updated 6.4 years ago by
GenoMax
140k • written 6.4 years ago by
Farbod
★ 3.4k
1
vote
23
replies
2.0k
views
FASTQ exctract ID's
fastq
4.3 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
3.6 years ago by
jmwhitha
• 0
6
votes
23
replies
2.9k
views
Could you help me set up a VCF filter?
genome
software error
VCF filter
5.8 years ago by
Charlie2
▴ 50
11
votes
22
replies
4.0k
views
No significant DEG: A request to double check my commands for limma.
limma
differential gene expression
covariates
4.9 years ago by
RNAseqer
▴ 260
23
votes
22
replies
48k
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 16 months ago by
Nicole
• 0 • written 5.9 years ago by
gaelgarcia
▴ 260
4
votes
22
replies
5.3k
views
samtools coverage usage
NGS
updated 2.8 years ago by
Lila M
★ 1.2k • written 2.8 years ago by
smrutimayipanda
▴ 20
1
vote
22
replies
3.4k
views
Genome Index and Alignment- STAR
RNA-Seq
genome
alignment
STAR
updated 5.3 years ago by
Kevin Blighe
87k • written 5.3 years ago by
carolgalah
• 0
3
votes
22
replies
3.0k
views
Making RefSeq in Windows
refseq
7.7 years ago by
Alireza Ebadi Tabrizi
• 0
2
votes
22
replies
2.2k
views
6 follow
Find ~1 Mb regions of genome that are shared by two or more WGS samples?
pedigree
linkage
genetics
17 months ago by
Joel Wallenius
▴ 210
0
votes
22
replies
3.3k
views
Using java Treeview to analyse genes: how to select and compile group of genes to present?
RNA-Seq
6.0 years ago by
Muha0216
• 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 effects
updated 6.5 years ago by
Biostar
20 • written 6.7 years ago by
lessismore
★ 1.3k
1
vote
22
replies
6.1k
views
how to use faSplit to split fasta into x files
next-gen
faSplit
sequence
5.4 years ago by
olechnwin
▴ 60
5
votes
22
replies
7.4k
views
SVM for classified gene expression data
R
svm
microarray
updated 20 months ago by
Ram
43k • written 8.2 years ago by
Shaurya Jauhari
▴ 50
5
votes
22
replies
3.3k
views
Differential analysis between two cell lines
R
RNA-Seq
edgeR
differential analysis
5.7 years ago by
Biologist
▴ 290
2
votes
21
replies
4.0k
views
Compute the correlations between submatrices
correlation
R
matrix
foreach
updated 5.0 years ago by
Ram
43k • written 5.0 years ago by
pablo
▴ 300
1
vote
21
replies
2.8k
views
Center and scale RIN values for DESeq2?
deseq2
rin
3.6 years ago by
randalljellis
▴ 90
6
votes
21
replies
2.7k
views
How to evaluate the similarity of genes between two sample
RNA-Seq
differential
updated 5.5 years ago by
Biostar
20 • written 5.7 years ago by
afli
▴ 190
16
votes
21
replies
2.1k
views
Why there are different hit for a same gene in different species
gene
blast
ortholog
paralog
7.5 years ago by
Farbod
★ 3.4k
3
votes
21
replies
3.7k
views
Normalization agilent microarray data?
Microarray
Normalization
updated 2.9 years ago by
Ram
43k • written 4.5 years ago by
mathavanbioinfo
▴ 80
7
votes
21
replies
3.1k
views
Merged.gtf vs. Rnor_6.0.gtf for Raw Counts
RNA-Seq
cuffmerge
raw counts
7.4 years ago by
jmsyl.hong
• 0
0
votes
21
replies
2.6k
views
HTSeq-Count: no_feature too high?
htseq-count
17 months ago by
sea.joson
▴ 10
1,000 results • Page
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Answer: diffbind : killed dba.count(DBsample, bParallel=FALSE)
Quantile normalizing prior to or after TPM scaling?
Structural variant filtering
Trouble with bedtools getfasta
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Answer: Hybrid assembly Pacbio- Nanopore
C: Why is 0/0 homozygous reference call in VCF useful information?
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Recent Replies
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
mRNA file is not going to have the same co-ordinates as the main chromosomes. Can you clarify what coordinates are in your BED file?
Comment: Downloading a list of all refseq assembly ids, including supressed assembliey
by
GenoMax
140k
Can you provide examples of suppressed ID's?
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
It is because I want to pull the mRNA fasta files and not DNA (which I guess is the case if I pull it from the entire genome)
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
If your intervals are for main chromosomes why are you using the mRNA file instead of the entire genome? If you have the gene ID's you coul…
Answer: diffbind : killed dba.count(DBsample, bParallel=FALSE)
by
Pierre Lindenbaum
160k
I downsampled the bams and it works now...
Answer: ONT direct RNA sequencing
by
dthorbur
★ 1.7k
You can check the validity of gzipped files using `gzip -v -t file.gz`. Should look something like this: ``` $ gzip -v -t test_file.…
Comment: Nanopore data filtering using fastp
by
emilydolivo97
• 0
I tested seqtk sample but I generate a wird result. Can I share my code and results with you please ?
Comment: Nextflow ERROR : Timeout waiting for connection from pool
by
GenoMax
140k
As best as I can tell it is a combination of things. Did you try setting `export NXF_ENABLE_VIRTUAL_THREADS="true"` in your shell? You also…
Comment: Coverage observed in introns in the Knockdown genes but not in knockout genes
by
rohitsatyam102
▴ 840
As per the image below obtained by Running RNASeQC the intronic reds aren't that much (See the knockdown samples enclosed in the Red box) (…
Comment: Parsing fasta file by coordinates
by
Joe
21k
Am I understanding this correctly, that what you are looking for is any sequence where *any part* of the coord range overlaps with *any oth…
Comment: convert cds to seurat object
by
edoardofilippi1998
• 0
Did you check the data in the assay of the cell_data_set object?
Comment: calculate mismatch rate from VCF file
by
Pierre Lindenbaum
160k
use the output of `samtools mpileup`
Comment: Volcano Plot Output Inquiry: Graphs Facing Down
by
ATpoint
81k
It's `-log10(pvalue)`, you miss the minus. Some people use indeed pvalue, but since you're filtering on padj, I would show `-log10(padj)` r…
Comment: calculate mismatch rate from VCF file
by
Dora
▴ 10
Thank you for your reply!! My bad. I didn't mention that I want to get the mismatch rate for each site. Is this error rate for each site?
Comment: Interproscan taking so much time
by
dthorbur
★ 1.7k
Parallelize. Chunk your transcriptome into groups of something like 5000 (or less if you want it to go faster), and run an array across you…
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