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121,546 results • Page
1764 of 2431
Sort: Rank
Rank
Views
Votes
Replies
5
votes
11
replies
3.0k
views
What's next differential expression?
DE
Differential expression
edgeR
RNA-Seq
updated 8.8 years ago by
Farbod
★ 3.4k • written 8.8 years ago by
germelcar
▴ 20
2
votes
2
replies
1.8k
views
Differentiation between a draft and whole genom
genome
updated 8.8 years ago by
lakhujanivijay
5.9k • written 8.8 years ago by
glady
▴ 320
1
vote
2
replies
4.2k
views
Meaning Of The Initial Column Of Filtered Out By Vcfutils.Pl Varfilter -P
samtools
mpileup
updated 8.8 years ago by
Biostar
20 • written 12.7 years ago by
bioinformatica2005
• 0
3
votes
3
replies
2.5k
views
small RNA-seq unique reads
alignment
small RNA-seq
8.8 years ago by
riccardo
▴ 90
0
votes
8
replies
2.3k
views
Detection of CNVs
CNVs
GATK
updated 8.8 years ago by
chen
★ 2.5k • written 8.8 years ago by
nkausthu
▴ 40
2
votes
2
replies
6.7k
views
How to make new VCF files myself?
VCF
Variant
VariantAnnotation
updated 8.8 years ago by
chen
★ 2.5k • written 8.9 years ago by
Amirosein
▴ 70
5
votes
2
replies
20k
views
What is a bam.bai for?
RNA-Seq
alignment
updated 8.8 years ago by
chen
★ 2.5k • written 8.8 years ago by
aswartz85
▴ 20
1
vote
3
replies
5.4k
views
ComBat (SVA) Application - Two Technical Effects
ComBat
sva
bioconductor
updated 3.3 years ago by
Ram
45k • written 10.5 years ago by
andrew.j.skelton73
6.6k
0
votes
0
replies
1.7k
views
Job:
Stanford Cancer Systems Biology Scholars Program, Stanford, CA, USA
cancer-biology
postdoc
updated 2.3 years ago by
Ram
45k • written 8.8 years ago by
tmccann
• 0
0
votes
10
replies
8.7k
views
Multiple paired-end gzipped fastq files as input into hisat2 error - fastq format not recognised
RNA-Seq
hisat2
fastq
gzip
list input
8.8 years ago by
nwon
▴ 60
2
votes
2
replies
2.1k
views
I have mRNA seq data from another lab that reports reads by RNA counts. How can I compare to my cufflinks data, which reports FPKM?
alignment
RNA-Seq
8.8 years ago by
aswartz85
▴ 20
0
votes
1
reply
2.4k
views
a5 assembly Error building contigs with IDBA
a5
de novo assembly
a5 Assembler
IDBA error
8.8 years ago by
kingcohn
▴ 30
1
vote
1
reply
3.0k
views
download exome bam files from 1000 genome project
bam
updated 8.8 years ago by
Jared Evans
▴ 80 • written 8.8 years ago by
simonjean434
▴ 70
0
votes
5
replies
11k
views
p value in box whisker
statstical
updated 8.8 years ago by
Ron
★ 1.2k • written 8.8 years ago by
rob.costa1234
▴ 310
0
votes
1
reply
1.3k
views
Predict efficacy of drug using Artificial Neural Network
gene
Assembly
8.8 years ago by
shahyashd95
• 0
3
votes
8
replies
3.1k
views
Popen Blat has different behavior than same syntax in shell
python
blat
8.8 years ago by
nchuang
▴ 260
10
votes
6
replies
2.3k
views
Job:
Bioinformatics Scientist with NGS expertise opportunity in the USA
gene
next-gen-sequencing
updated 2.3 years ago by
Ram
45k • written 8.8 years ago by
susan
▴ 30
0
votes
1
reply
2.2k
views
Bowtie -m and -v parameter equivalent in bowtie2?
Bowtie
Bowtie2
alignment
updated 8.8 years ago by
Devon Ryan
105k • written 8.8 years ago by
datascientist28
▴ 570
0
votes
0
replies
2.0k
views
Pindel vcf tag HOMLEN?
Pindel
vcf
HOMLEN
HRun
Homopolymer run
updated 8.8 years ago by
Biostar
20 • written 9.0 years ago by
Jackie
▴ 70
2
votes
1
reply
7.8k
views
merge pdb chains
clustering
pdb
updated 2.0 years ago by
Ram
45k • written 8.9 years ago by
galleria123
• 0
3
votes
2
replies
3.9k
views
Comparing the output from DESeq and DESeq2
RNA-Seq
updated 8.8 years ago by
igor
13k • written 8.8 years ago by
bioinforesearchquestions
▴ 370
2
votes
1
reply
1.3k
views
Could you list some tools which take read-reference mapping as input?
gene
next-gen
sequence
updated 2.0 years ago by
Ram
45k • written 8.8 years ago by
manetsus
▴ 40
0
votes
0
replies
1.7k
views
Very few assigned reads in MEGAN
RNA-Seq
8.8 years ago by
dazhudou1122
▴ 140
2
votes
2
replies
1.9k
views
CWL : default value and label for argument
Common-Workflow-Language
cwl
updated 22 months ago by
Ram
45k • written 8.8 years ago by
sebastien.letort
▴ 70
11
votes
6
replies
3.3k
views
How can I separate a FASTA file into multiple exon and CDS files?
python
genome
fasta
annotation
sequence
updated 8.8 years ago by
glihm
▴ 660 • written 8.8 years ago by
anonymous1192976466
▴ 50
4
votes
1
reply
9.6k
views
What are RMA units?
rma
affymetrix
array
8.8 years ago by
lotus28
▴ 70
1
vote
3
replies
1.5k
views
upstream open reading frame gene filteration
RNA-Seq
8.8 years ago by
ashkan
▴ 160
0
votes
0
replies
3.4k
views
How can I use TCGA CNV data to analyse the copy number variation of a specific region(e.g. 8q24.11) in ovarian cancer patients?
genome
CNV
8.8 years ago by
Ashleyca
• 0
6
votes
7
replies
1.8k
views
picard-tool markduplicate gets stuck in traversing
picard tools
8.8 years ago by
blur
▴ 280
7
votes
0
replies
1.8k
views
News:
First PacBio Sequel data available
pacbio
sequel
updated 2.3 years ago by
Ram
45k • written 8.8 years ago by
GenoMax
152k
1
vote
2
replies
2.1k
views
News:
Making efficient NGS data analysis softwares - GATB-Core Library Tutorial
next-gen
GATB
updated 2.3 years ago by
Ram
45k • written 8.8 years ago by
patrick.durand
▴ 140
0
votes
1
reply
4.1k
views
How to get expression set from GSE?
affymetrix
gse
GEO
R
8.8 years ago by
lotus28
▴ 70
2
votes
4
replies
5.2k
views
Failed to process file in fastqc
next-gen
8.8 years ago by
mehar.27march
▴ 10
1
vote
1
reply
1.6k
views
Software for SNP analysis that can deal with ambiguities
SNP
sequence
updated 8.8 years ago by
EagleEye
7.6k • written 8.8 years ago by
NoaG
• 0
0
votes
1
reply
2.3k
views
Problem with ArrayExpress() command. Please help ..
R
updated 8.8 years ago by
deepue
▴ 160 • written 8.8 years ago by
Pijush Das
▴ 10
1
vote
3
replies
3.5k
views
Affy old package installation in R
R
updated 8.8 years ago by
deepue
▴ 160 • written 8.8 years ago by
jk
• 0
0
votes
3
replies
2.3k
views
How to find out the specific strain in NGS data?
phage
blast
bacteriophage
8.8 years ago by
lakhujanivijay
5.9k
4
votes
1
reply
10k
views
Need help with heatmaps in R, how to draw select genes or selected pathway??
RNA-Seq
DESEQ2
R
heatmap
ontology
updated 8.8 years ago by
Biostar
20 • written 8.8 years ago by
marina.kimyr
▴ 20
0
votes
0
replies
1.5k
views
Errors coming up in filtered SOLiD csfasta reads after using SOLiD_preprocess_filter_v2.pl
RNA-Seq
software error
next-gen
8.8 years ago by
zainab12khanum
• 0
1
vote
6
replies
2.8k
views
error: argument --reference is required
cwl
updated 8.8 years ago by
Ram
45k • written 8.8 years ago by
giuseppacefalu
• 0
3
votes
4
replies
2.3k
views
about computer memory and mpileup files
SNP
memory
varscan2
updated 8.8 years ago by
karl.stamm
4.1k • written 8.8 years ago by
Bogdan
★ 1.4k
5
votes
1
reply
3.0k
views
differential methylation of illumina 450k data
sequencing
methylation
450k
illumina
updated 8.8 years ago by
Charles Warden
8.3k • written 8.8 years ago by
Govardhan Anande
▴ 150
0
votes
0
replies
883
views
Rare Variant Burden tool that can also output the contingency
sequence
genome
sequencing
next-gen
R
8.8 years ago by
brend.k.bk
• 0
3
votes
2
replies
2.6k
views
PE read flag 69 and 137 meaning
sam
flag
updated 8.8 years ago by
harold.smith.tarheel
★ 5.0k • written 8.8 years ago by
epigene
▴ 590
1
vote
0
replies
2.1k
views
Underestimating heterozygotes in variant calling in FreeBayes
next-gen
SNP
freebayes
variant calling
8.8 years ago by
crossman.ca
▴ 10
1
vote
3
replies
2.4k
views
Read counts mapping against rrna genes in prokaryotic RNA-Seq experiment
RNA-Seq
bacteria
TopHat
updated 2.3 years ago by
Ram
45k • written 8.8 years ago by
buthercup_ch
▴ 30
0
votes
5
replies
1.7k
views
Identifying my WGS isolates
next-gen
blast
Assembly
updated 8.8 years ago by
Tonor
▴ 480 • written 8.8 years ago by
jeancampbell212121
• 0
2
votes
3
replies
3.9k
views
CG Target IDS from Illumina 450k
CG
Gene Coordinates
Illumina 450k
updated 8.8 years ago by
mastal511
★ 2.1k • written 8.8 years ago by
questionaire
• 0
8
votes
3
replies
2.3k
views
News:
Impact of outdated gene annotations on pathway enrichment analysis
pathway-enrichment
gene-ontology
david
go
updated 2.3 years ago by
Ram
45k • written 8.8 years ago by
pld
5.1k
3
votes
2
replies
4.1k
views
Duplicate miRNAs with different read counts in miRDeep2
miRDeep2
miRNA
miRNAs
miRDeep
Read counts
updated 8.8 years ago by
benformatics
4.1k • written 8.8 years ago by
PAn
▴ 20
121,546 results • Page
1764 of 2431
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A: Get closest taxa of a target species in a phylogeny
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Recent Replies
Comment: Extract track data from "search by region" feature on ENCODE
by
GenoMax
152k
Examples of the API don't show any region based examples. Not saying that is not possible but it would be an obvious example that would hav…
Comment: Draw GO tree for some GO ids with coloring
by
boczniak767
▴ 880
Thank you all for input. @jaredandrews07 - I have too many graphs to color them manually ;-). It is not the first time when I find answer …
Answer: Weird p-value distribution on edgeR results
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15k
> On the other hand, it is possible to get an p-value histogram like you show if there is a massive batch effect and the batch effect is ba…
Answer: Draw GO tree for some GO ids with coloring
by
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Frankly, I'd just get as close as possible and then re-color the significant terms in Illustrator or such. [genescape](https://github.co…
Answer: Extract transcript fasta using gff
by
cmdcolin
★ 4.2k
As long as this thread is revived, there is minigff now also https://github.com/lh3/minigff For gffread, the documentation for some reason…
Answer: Draw GO tree for some GO ids with coloring
by
txema.heredia
▴ 250
`clusterProfiler` has several tools to draw the results: https://yulab-smu.top/biomedical-knowledge-mining-book/enrichplot.html Even …
Comment: RNA seq strandedness (reverse-strand)
by
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★ 4.0k
You can use [IGV][1] to look at your alignment using your reference and its gene-annotation. You'll see how your reads orient themselves in…
Comment: Identifying gene outliers in a genome using composition analysis.
by
Shakunthala Natarajan
• 0
Thank you. I will check them out.
Comment: RNA seq strandedness (reverse-strand)
by
GenoMax
152k
Use a standard tool like `featureCounts` as noted here --> https://www.biostars.org/p/9612088/#9612095
Comment: RNA seq strandedness (reverse-strand)
by
ZuelTech
• 0
I actually used STAR tool to align it to viral genomes.
Answer: Problem with Mirdeep2 and Randfold output
by
Jasim
• 0
At the moment the corresponding server is down I emailed to corresponder but He/ she on vacations till midsummer.. I am in the same boat.. …
Answer: Extract transcript fasta using gff
by
Bourumir
▴ 10
*gffread* is generally the right tool, but it does not produce the gene map required by downstream tools such as Salmon. Additionally, with…
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166k
if you use the same filtering and `samtools depth -a ` there should be no difference isn't it ? samtools coverage would be faster.
Answer: RNA seq strandedness (reverse-strand)
by
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★ 4.0k
It depends on the alignment method you used. If you aligned against the transcriptome, you can do it that way you described. In case you al…
Comment: Trouble getting representatives from clustered_nr database
by
Adolfo
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It was indeed huge, for viridiplantae we have ``` $ wc -l Viridiplantae_representative_cluster.txt 16968635 Viridiplantae_representative_…
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