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1,000 results • Page
2 of 20
Sort: Votes
Rank
Views
Votes
Replies
12
votes
10
replies
3.5k
views
Speed up BLASTp vs NCBI nr database
blast
6.7 years ago by
biotech
▴ 560
12
votes
13
replies
2.1k
views
Gene Expression and Systems Biology (homework)
gene
homework
updated 7 weeks ago by
Ram
37k • written 7.6 years ago by
sarathkurichiyil
• 0
11
votes
22
replies
2.7k
views
No significant DEG: A request to double check my commands for limma.
limma
differential gene expression
covariates
3.8 years ago by
RNAseqer
▴ 220
11
votes
10
replies
9.7k
views
Extracting from tophat outputs reads pairs and splice-junctions with a single best match
TOPHAT
RNA-Seq
updated 13 months ago by
Ram
37k • written 8.4 years ago by
trakhtenberg
▴ 160
11
votes
12
replies
939
views
Need help changing RNA-seq code from histat aligner into Star aligner please.
RNA-Seq
2.6 years ago by
screadore
▴ 20
11
votes
2
replies
1.3k
views
Concept behind p-value correction?
RNA-Seq
protemics
genome
R
3.5 years ago by
WUSCHEL
▴ 660
11
votes
10
replies
2.2k
views
6 follow
Genomic statistics from gtf
gene
gtf
4.6 years ago by
plebaninora
• 0
11
votes
4
replies
2.3k
views
10 to 1000X speedup of BWA read alignment trough compressive mapping: MIT CORA
bwa
fastq
alignment
compression
updated 6.6 years ago by
Biostar
20 • written 6.8 years ago by
William
★ 5.1k
11
votes
11
replies
4.6k
views
6 follow
How to get work experience in Bioinformatics
work experience
python
genome
sequence
4.9 years ago by
ishackm
▴ 110
11
votes
9
replies
2.0k
views
samtools piping with awk/ bash commands -> Wonky things happen!!!
bash
samtools
awk
updated 5 weeks ago by
Ram
37k • written 7.6 years ago by
QVINTVS_FABIVS_MAXIMVS
★ 2.5k
11
votes
5
replies
824
views
Differential expression analysis - issue with replicating results
rnaseq
DESeq2
R
bioconductor
updated 14 months ago by
ATpoint
68k • written 14 months ago by
suzanne rein
▴ 10
11
votes
11
replies
2.3k
views
Error of Groups in R
affy
limma
oligo
bioconductor
R
updated 6.7 years ago by
Biostar
20 • written 6.7 years ago by
12021560-040
▴ 70
11
votes
15
replies
2.2k
views
How do I get the read counts for a specific exon
bam
exon
updated 4.8 years ago by
Ram
37k • written 4.8 years ago by
b10hazard
▴ 30
11
votes
11
replies
596
views
6 follow
Doubt regarding dna sequence length
genome
sequencing
sequence
2.8 years ago by
lokeshp14cs24
• 0
11
votes
29
replies
7.8k
views
SummarizedExperiment nrow differs from ncol
DESeq2
SummarizedExperiment
updated 15 months ago by
Ram
37k • written 8.6 years ago by
Parham
★ 1.6k
11
votes
10
replies
1.2k
views
Most fishes lay eggs, some are live-bearing, How to find related genes to these different charachteristics?
gene
reproduction
evolution
alignment
updated 6.4 years ago by
Biostar
20 • written 6.4 years ago by
Farbod
★ 3.3k
11
votes
7
replies
2.9k
views
Estimating Mean Inner Distance
tuxedo
tophat
RNA-Seq
6.2 years ago by
CF
▴ 50
11
votes
10
replies
4.9k
views
Best mapping software to generate BAM file
BAM
mapping
updated 5.2 years ago by
Biostar
20 • written 5.3 years ago by
Anand Rao
▴ 550
11
votes
24
replies
3.8k
views
BWA mem skip orientation
assembly
genome
alignment
next-gen
3.8 years ago by
williamsbrian5064
▴ 470
10
votes
8
replies
5.6k
views
Software To Calculate Power Of Exome Sequencing?
exome
statistics
updated 11.4 years ago by
Neilfws
49k • written 11.4 years ago by
Liyf
▴ 300
10
votes
21
replies
2.2k
views
Calculate disease risk based on the genoytype of some SNPs?
SNP
prs
gwas
PRSice
Plink
updated 3.5 years ago by
Biostar
20 • written 3.5 years ago by
Miguel
▴ 10
10
votes
8
replies
1.4k
views
File Format - Fasta
sequence
6.9 years ago by
Gabe Anderson
▴ 10
10
votes
7
replies
884
views
Can two mates have different file size?
sequencing
fastq
4.5 years ago by
marongiu.luigi
▴ 670
10
votes
11
replies
5.2k
views
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
RNA-Seq
QC
4.3 years ago by
jackgrayner
▴ 50
10
votes
1
reply
3.7k
views
Assessing The Quality Of Mirna Rnaseq Data
mirna
updated 9.2 years ago by
Biostar
20 • written 9.9 years ago by
Ashutosh Pandey
12k
10
votes
13
replies
5.1k
views
How to identify DE lncRNA from RNA Seq Data?
RNA-Seq
lncrna
5.9 years ago by
Vasu
▴ 720
10
votes
5
replies
5.1k
views
Intron Retention And Alternative 5'3' Splice Site Identification
updated 9.0 years ago by
Biostar
20 • written 11.8 years ago by
Arun
2.4k
10
votes
7
replies
3.2k
views
What is Pathway Analysis?
pathway
analysis
ontology
database
tools
6.8 years ago by
Pranavathiyani G
▴ 330
10
votes
10
replies
1.5k
views
Minor allele frequency
GWAS
SNPs
Alleles
updated 4.2 years ago by
Biostar
20 • written 6.2 years ago by
alessandrotestori7
▴ 410
10
votes
2
replies
332
views
any script that can do this task
shell-script
updated 10 months ago by
Ram
37k • written 10 months ago by
adyashapanda04
▴ 10
10
votes
5
replies
6.1k
views
how to remove asterisk characters from a translated sequences (fasta format)?
sequencing
Assembly
alignment
updated 5 months ago by
Ram
37k • written 7.4 years ago by
seta
★ 1.7k
10
votes
23
replies
1.7k
views
Two simillarly annotated sequence has no alignment similarity. Why?
blast
alignment
gene
updated 5.2 years ago by
GenoMax
125k • written 5.2 years ago by
Farbod
★ 3.3k
10
votes
9
replies
1.5k
views
How to improve fastq quality based on fastqc output ?
RNA-Seq
4.7 years ago by
Angelique
▴ 10
10
votes
12
replies
1.4k
views
The 2013 Eisenberg and Levanon housekeeping genes list for Human is the most updated one?
genes
human
housekeeping
list
4.0 years ago by
msimmer92
▴ 300
10
votes
10
replies
3.1k
views
Parameter optimization STAR
RNA-Seq
4.9 years ago by
XBria
▴ 90
10
votes
3
replies
1.2k
views
how to create new file
r
updated 6.2 years ago by
GenoMax
125k • written 6.2 years ago by
forever
▴ 80
10
votes
11
replies
4.1k
views
Trouble Installing Genometools-1.5.1 On My Mac Ox
genome
protein-structure
9.0 years ago by
inadamj
▴ 60
10
votes
7
replies
911
views
Better DE analytic tools
RNA-Seq
DE tools
Bayesian empirical approach
4.7 years ago by
mhyunjunkang
▴ 110
10
votes
14
replies
3.4k
views
ATAC-seq data and deepTools: Small detail with impact on output
deeptools
ATACseq
bigwig
readlength
Forum
updated 3.0 years ago by
ATpoint
68k • written 3.0 years ago by
gable_works
▴ 50
10
votes
11
replies
8.1k
views
How to adjust my manhattan plot to look better?
qqman
manhattan
R
updated 8 months ago by
Ram
37k • written 7.9 years ago by
SheelS
▴ 40
10
votes
6
replies
2.5k
views
which language to use for such a bioinformatics web services infrastructure?
web services
bioinformatics
java
infrastructure
7.7 years ago by
lait
▴ 170
10
votes
15
replies
5.0k
views
convert fasta/gb to vcf
vcf
reference
file conversion
4.3 years ago by
marongiu.luigi
▴ 670
10
votes
2
replies
2.6k
views
Standalone Blast Issue
blast
10.7 years ago by
chlazaris
• 0
10
votes
5
replies
2.2k
views
error with samtools
RNA-Seq
updated 6.0 years ago by
Biostar
20 • written 6.1 years ago by
mra8187
▴ 20
10
votes
19
replies
2.3k
views
What is a difference between uniprot and 'nr. Non-redundant GenBank...'?
Genebank
blast
UniProt
updated 20 months ago by
GenoMax
125k • written 20 months ago by
matt
▴ 20
10
votes
11
replies
1.2k
views
How to identify dysregulated pathways using Support Vector machine (SVM)?
SVM
4.1 years ago by
Chaimaa
▴ 260
10
votes
15
replies
5.4k
views
DIAMOND blast imported into MEGAN6 has no taxonomic assignment
blast
MEGAN6
Taxonomy
DIAMOND
6.2 years ago by
Farbod
★ 3.3k
10
votes
8
replies
1.8k
views
Blast scores...two annotations for the same piece of sequence
alignment
updated 7 months ago by
Ram
37k • written 7.8 years ago by
friasoler
▴ 30
10
votes
4
replies
957
views
How to pipe samtools mileup with varscan trio caller?
varscan
samtools
pipe
2.0 years ago by
dare_devil
★ 1.7k
10
votes
25
replies
2.5k
views
The interpretation of PCA
DESeq2
R
PCA
updated 4.5 years ago by
Biostar
20 • written 4.6 years ago by
Za
▴ 140
1,000 results • Page
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Recent Votes
Answer: Looking for a tool which provides mapping quality score distributions from BAM f
Comment: mirbase does not have miRNA annotation of my species, what are the alternatives?
Answer: mirbase does not have miRNA annotation of my species, what are the alternatives?
Answer: Gviz python alternative
Answer: Gviz python alternative
Answer: Annotating snps with gene information
Comment: Plotting Correlation matrix
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Answer: Python Dictionary of Primer3-py Primer Designs
by
barslmn
★ 1.2k
You're so close. You can simply loop over sequence dictionaries like you did with the `design_output` and check if the keys with `startswit…
Comment: Unable to install clusterProfiler on Mac M1
by
GenoMax
125k
Have you installed `Xcode` and the command line tools that go with? If not you will need to install those.
Answer: SRA taxonomy analysis
by
Steve
• 0
Thanks @genomax I created an aws glue crawler to pull the data from s3://sra-pub-metadata-us-east-1/sra_tax_analysis_tool/ I wonder if it …
Comment: mirbase does not have miRNA annotation of my species, what are the alternatives?
by
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thanks! however, shouldn't it also have a gtf/gff file with the annotations?
Comment: Getting a VCF file from plink .bed, .fam and .bim files
by
hi.there
• 0
Thanks Ram. Yes. I have read all of this documentation before. --file and --bfile. I have actually tried doing the complete liftover be…
Answer: SRA taxonomy analysis
by
GenoMax
125k
This data may only be available using `BigQuery` for [**SRA in cloud**][1]. For more information on querying: https://www.ncbi.nlm.nih.g…
Comment: MesKit error message - Join columns must be present in data.
by
CH1374
• 0
column names for the maf are: [1] "Hugo_Symbol" "Chromosome" "Start_Position" [4] "End_Position" "Variant_Classification" "Variant_Type" [7…
Answer: scaffold assembly inro chromosomal assembly using reference genome
by
samuel.a.odonnell
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Have a look at ragtag and ragout. I use ragout for smaller assemblies (~20 Mb and less) and ragtag for larger genomes.
Comment: CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRl
by
Ram
37k
I've been meaning to work on a Biostars-specific code formatting manual for a while now but the basic is pretty simple: You can use backtic…
Comment: Multiline Fasta To Single Line Fasta
by
Onur
• 0
Thank you it's also worked for me too. Best,
Comment: CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRl
by
Estefania
▴ 10
Thanks Ram. Could you point to a manual on how to make the post look like yours? I just copy-pasted my R script and this is how it shows in…
Comment: extracting input files form Seurat
by
rasing02
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Thank you jared.andrews07
Comment: extracting input files form Seurat
by
rasing02
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Yes, I just need the input data so that investigators can use tools other than R to visualize the data in form of viloin plots or feature p…
Comment: Downloading 450k methylation data from GEO
by
GenoMax
125k
I don't think they have provided processed data as a single upload.
Answer: extracting input files form Seurat
by
jared.andrews07
★ 14k
You can get the data behind any of the plots easily enough: ``` p <- VlnPlot(Seurat_object, features = "X", group.by = "Names",split.by…
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