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1,000 results • Page
2 of 20
Sort: Votes
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Views
Votes
Replies
12
votes
10
replies
4.2k
views
Speed up BLASTp vs NCBI nr database
blast
8.0 years ago by
biotech
▴ 570
12
votes
17
replies
4.9k
views
How do I generate all possible Newick Tree permutations for a set of species given an outgroup in Python?
Python
Newick
phylogenetics
tree
phylogeny
6.6 years ago by
anonymous1192976466
▴ 50
12
votes
28
replies
2.8k
views
Calculating the expression level of genes
Gene expression
RNA-Seq
R
5.9 years ago by
Za
▴ 140
12
votes
10
replies
2.9k
views
7 follow
SAM / BAM alignments
SAM
BAM
7.4 years ago by
John
13k
12
votes
21
replies
3.3k
views
Calculate disease risk based on the genoytype of some SNPs?
SNP
prs
gwas
PRSice
Plink
updated 4.8 years ago by
Biostar
20 • written 4.8 years ago by
Miguel
▴ 30
12
votes
12
replies
5.0k
views
Need A Script That Finds Whether A String In One Column Matches In Other Columns Of The Same Row
perl
updated 10.5 years ago by
Istvan Albert
100k • written 10.5 years ago by
biolab
★ 1.4k
12
votes
8
replies
1.3k
views
Align 16S sequence to a reference
16S
sequence
alignment
updated 20 months ago by
Matthias Zepper
4.6k • written 20 months ago by
A_heath
▴ 160
12
votes
14
replies
5.8k
views
bedtools intersect error?
ChIP-Seq
bedtools
intersect
5.2 years ago by
star
▴ 350
12
votes
11
replies
3.3k
views
How To Get Snp Genotypes
snp
genotyping
updated 12.7 years ago by
Lars Juhl Jensen
11k • written 13.1 years ago by
Pri
▴ 20
12
votes
8
replies
3.2k
views
How to change depth of sequence in RNA-seq fastq files
depth of sequence
RNA-Seq
7.3 years ago by
statfa
▴ 760
11
votes
22
replies
4.3k
views
No significant DEG: A request to double check my commands for limma.
limma
differential-gene-expression
updated 5 weeks ago by
Ram
43k • written 5.1 years ago by
RNAseqer
▴ 270
11
votes
10
replies
10k
views
Extracting from tophat outputs reads pairs and splice-junctions with a single best match
TOPHAT
RNA-Seq
updated 2.4 years ago by
Ram
43k • written 9.8 years ago by
trakhtenberg
▴ 160
11
votes
12
replies
1.4k
views
Need help changing RNA-seq code from histat aligner into Star aligner please.
RNA-Seq
3.9 years ago by
screadore
▴ 20
11
votes
2
replies
1.5k
views
Concept behind p-value correction?
RNA-Seq
protemics
genome
R
4.8 years ago by
WUSCHEL
▴ 760
11
votes
10
replies
5.8k
views
Best mapping software to generate BAM file
BAM
mapping
updated 6.5 years ago by
Biostar
20 • written 6.6 years ago by
Anand Rao
▴ 630
11
votes
9
replies
2.5k
views
samtools piping with awk/ bash commands -> Wonky things happen!!!
bash
samtools
awk
updated 17 months ago by
Ram
43k • written 8.9 years ago by
QVINTVS_FABIVS_MAXIMVS
★ 2.5k
11
votes
11
replies
1.1k
views
6 follow
Doubt regarding dna sequence length
genome
sequencing
sequence
4.1 years ago by
lokeshp14cs24
• 0
11
votes
24
replies
5.5k
views
BWA mem skip orientation
assembly
genome
alignment
next-gen
5.1 years ago by
williamsbrian5064
▴ 520
11
votes
6
replies
6.3k
views
Merging raw Illumina FASTQ files with snakemake
snakemake
illumina
paired-end reads
6.9 years ago by
Jokhe
▴ 140
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
11
votes
6
replies
3.3k
views
Understanding Supplementary reads.
Bowtie2
MEM
BWA
Dragen
updated 2.3 years ago by
Istvan Albert
100k • written 2.3 years ago by
kiran
▴ 10
11
votes
7
replies
3.3k
views
Estimating Mean Inner Distance
tuxedo
tophat
RNA-Seq
7.5 years ago by
CF
▴ 50
11
votes
5
replies
1.3k
views
Differential expression analysis - issue with replicating results
rnaseq
DESeq2
R
bioconductor
updated 2.5 years ago by
ATpoint
82k • written 2.5 years ago by
suzanne rein
▴ 10
11
votes
3
replies
999
views
How to deal with the probe id mapping to multiple gene ids?
match
microarray
affymetrix
probe
gene
13 months ago by
DareDevil
★ 4.3k
11
votes
11
replies
5.7k
views
6 follow
How to get work experience in Bioinformatics
work experience
python
genome
sequence
6.2 years ago by
ishackm
▴ 110
11
votes
11
replies
2.8k
views
Error of Groups in R
affy
limma
oligo
bioconductor
R
updated 8.0 years ago by
Biostar
20 • written 8.0 years ago by
12021560-040
▴ 70
11
votes
10
replies
2.8k
views
6 follow
Genomic statistics from gtf
gene
gtf
5.9 years ago by
plebaninora
• 0
11
votes
4
replies
2.6k
views
10 to 1000X speedup of BWA read alignment trough compressive mapping: MIT CORA
bwa
fastq
alignment
compression
updated 7.9 years ago by
Biostar
20 • written 8.1 years ago by
William
★ 5.3k
11
votes
15
replies
2.9k
views
How do I get the read counts for a specific exon
bam
exon
updated 6.2 years ago by
Ram
43k • written 6.2 years ago by
b10hazard
▴ 30
11
votes
10
replies
1.6k
views
Most fishes lay eggs, some are live-bearing, How to find related genes to these different charachteristics?
gene
reproduction
evolution
alignment
updated 7.7 years ago by
Biostar
20 • written 7.7 years ago by
Farbod
★ 3.4k
10
votes
8
replies
6.1k
views
Software To Calculate Power Of Exome Sequencing?
exome
statistics
updated 12.7 years ago by
Neilfws
49k • written 12.7 years ago by
Liyf
▴ 300
10
votes
7
replies
1.3k
views
Can two mates have different file size?
sequencing
fastq
5.8 years ago by
marongiu.luigi
▴ 710
10
votes
5
replies
2.4k
views
error with samtools
RNA-Seq
updated 7.3 years ago by
Biostar
20 • written 7.4 years ago by
mra8187
▴ 20
10
votes
9
replies
2.0k
views
How to improve fastq quality based on fastqc output ?
RNA-Seq
6.0 years ago by
Angelique
▴ 10
10
votes
15
replies
6.2k
views
DIAMOND blast imported into MEGAN6 has no taxonomic assignment
blast
MEGAN6
Taxonomy
DIAMOND
7.5 years ago by
Farbod
★ 3.4k
10
votes
3
replies
1.4k
views
how to create new file
r
updated 7.5 years ago by
GenoMax
142k • written 7.5 years ago by
forever
▴ 80
10
votes
4
replies
1.4k
views
How to pipe samtools mileup with varscan trio caller?
varscan
samtools
pipe
3.3 years ago by
DareDevil
★ 4.3k
10
votes
1
reply
4.0k
views
Assessing The Quality Of Mirna Rnaseq Data
mirna
updated 10.5 years ago by
Biostar
20 • written 11.2 years ago by
Ashutosh Pandey
12k
10
votes
6
replies
995
views
RNA seq, secreted protein
protein
gene
secreted
updated 9 months ago by
Joe
21k • written 17 months ago by
Rob
▴ 170
10
votes
1
reply
3.5k
views
RNA-SeQC, EVER-seq, RSeQC and CollectRnaSeqMetrics, which to use and *why*?
RNA-Seq
qc
updated 21 months ago by
Ram
43k • written 9.0 years ago by
Niek De Klein
★ 2.6k
10
votes
12
replies
2.0k
views
The 2013 Eisenberg and Levanon housekeeping genes list for Human is the most updated one?
genes
human
housekeeping
list
5.3 years ago by
msimmer92
▴ 300
10
votes
15
replies
6.3k
views
convert fasta/gb to vcf
fasta
vcf
genbank
gff
updated 14 months ago by
Ram
43k • written 5.6 years ago by
marongiu.luigi
▴ 710
10
votes
15
replies
1.8k
views
Can't find a variant which suppose must have in a vcf file
variant-calling
bcftools
nf-core
11 months ago by
Chris
▴ 280
10
votes
10
replies
2.1k
views
PyWGCNA
WGCNA
11 months ago by
yoshifumimiya
▴ 50
10
votes
19
replies
3.5k
views
What is a difference between uniprot and 'nr. Non-redundant GenBank...'?
Genebank
blast
UniProt
updated 3.0 years ago by
GenoMax
142k • written 3.0 years ago by
matt
▴ 20
10
votes
11
replies
4.7k
views
Trouble Installing Genometools-1.5.1 On My Mac Ox
genome
protein-structure
10.3 years ago by
inadamj
▴ 60
10
votes
14
replies
5.0k
views
ATAC-seq data and deepTools: Small detail with impact on output
bigwig
read-length
deeptools
ATAC-seq
updated 11 months ago by
Ram
43k • written 4.3 years ago by
gable_works
▴ 50
10
votes
6
replies
8.5k
views
Any idea how to solve this error in fgsea - "Error in if (any(simpleFgseaRes$modeFraction < 10)) { : missing value where TRUE/FALSE needed"?
fgsea
updated 2.9 years ago by
alserg
▴ 930 • written 2.9 years ago by
gabrielbaldanzi
▴ 10
10
votes
13
replies
5.8k
views
How to identify DE lncRNA from RNA Seq Data?
RNA-Seq
lncrna
7.2 years ago by
Vasu
▴ 770
10
votes
23
replies
2.5k
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
1,000 results • Page
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Recent Votes
A: How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Seque
C: Snakemake vs. Nextflow: strengths and weaknesses
Answer: workflow management system : WDL, CWL, Ruffus, SnakeMake, etc
Sequence alignment on split read event such as inversion, duplication and complex nested events.
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
Comment: Add stats to the plot
Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
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Recent Awards •
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Scholar
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161k
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▴ 30
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Recent Replies
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Luqman
• 0
I am using *pybiomart* which has Server inplace of BiomartServer, I used that as per above but still getting the same error. Also, when I a…
Comment: Blastn, need help to increase speed
by
m13113153781
• 0
mmseq2 is indeed a good acceleration solution, but its index files require ~ 6 T space....
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
KHURRAM SHAHZAD
• 0
Thank you it works
Answer: Add stats to the plot
by
Ghada
• 0
I think this is what caused the error. we do not have group 1 and 2 in the statistical test results???? ![enter image description here][…
Answer: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
Bibi
• 0
@atpoint thanks you for your timely response. Can someone else shed light if we can compare the trend of DEGs using the scRNA and Bulk RNA…
Comment: Add stats to the plot
by
GenoMax
142k
Please use `101010` to format `code` so it is represented in monospace font. I have done this for you now.
Answer: is there a tool to recover corrupted fastq files
by
Tommaso
• 0
You may also want to give a try to **FastqWiper** (https://github.com/mazzalab/fastqwiper)
Comment: Add stats to the plot
by
Ghada
• 0
Thanks. That helpful. I am getting this error data4_test <- data4.ts%>% ungroup() %>% t.test(data =.,value ~ Condition)%>% + …
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
ATpoint
82k
I cannot comment here. You are asking why results between two experiments are different. I do not know without seeing the data.
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
Bibi
• 0
Thank you so much for this insight. I just want to clarify another point here. I have used scRNA seq data from mice mammary epithelial cell…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
> Cannot read non-existent file: file:///local/home/User/VCF_Filtering/biostar.code your file doesn't exist, is at the wrong place etc.
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
• 0
Hi Pierre, I am attempting to run this code and am running into this error: (jvar) $ jvarkit vcffilterjdk -f biostar.code Dart_VCF2_Or…
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
ATpoint
82k
I cannot give a precise answer, as ML is not my field, but generally, why don't you apply the method to pseudobulks of the exact single-cel…
Answer: geom_bar issue in ggplot2 with xlim()
by
ATpoint
82k
https://stackoverflow.com/questions/10365167/geom-bar-bars-not-displaying-when-specifying-ylim
Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
▴ 50
Yes. We are sequencing 45 different samples with illumina. 12 of these are also going to be sequenced with Nanopore (for hybrid assembly). …
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