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121,546 results • Page
1784 of 2431
Sort: Rank
Rank
Views
Votes
Replies
2
votes
0
replies
1.8k
views
4C/5C Interaction Data from RoadMap
Long range interaction
4c
5C
HiC
8.9 years ago by
Chirag Nepal
★ 2.4k
1
vote
9
replies
2.8k
views
Are old versions of NCBI's nt stored somewhere?
RNA-Seq
blast
software error
genome
rna-seq
8.9 years ago by
felix.kuo.1211
▴ 10
2
votes
10
replies
2.1k
views
Use of Bowtie2 in NGS
RNA-Seq
updated 8.9 years ago by
Medhat
9.8k • written 8.9 years ago by
p.prakash.saurabh
• 0
2
votes
4
replies
3.1k
views
problem in Abundance Estimation using RSEM
Assembly
RNA-Seq
software error
updated 8.9 years ago by
WouterDeCoster
48k • written 8.9 years ago by
bilal.sarwar
▴ 10
0
votes
0
replies
2.2k
views
Genome STRiP execution time
Genome-STRiP
runtime
1000genomes
GATK
updated 3.3 years ago by
Ram
45k • written 10.6 years ago by
eyb
▴ 270
4
votes
4
replies
2.2k
views
Use BLAST algorithms to discover function of a gene
blast
updated 8.9 years ago by
natasha.sernova
★ 4.0k • written 8.9 years ago by
Bilal
▴ 60
0
votes
4
replies
1.9k
views
Is there a way to extract sites that are perfectly aligned to the reference genome in maf format?
alignment
8.9 years ago by
Cacau
▴ 520
0
votes
0
replies
1.7k
views
Quite low mapping efficient for single-cell methylation sequencing data
single-cell BS-seq
SRA
mapping ratio
8.9 years ago by
Shicheng Guo
★ 9.6k
8
votes
7
replies
7.5k
views
I got low overall alignment rate running HiSAT2
RNA-Seq
hisat
hisat2
alignment
8.9 years ago by
sslee1015
• 0
0
votes
1
reply
3.2k
views
unmapped reads from Tophat
tophat
alignment
updated 8.9 years ago by
WouterDeCoster
48k • written 8.9 years ago by
maheetha.b
▴ 70
0
votes
2
replies
4.0k
views
mirdeep2 error in sequence file
next-gen
mirdeep2
ngs
updated 8.9 years ago by
gzl
▴ 20 • written 9.1 years ago by
kamyasingh2490
• 0
10
votes
2
replies
9.4k
views
Problems With Mirdeep2
hg19
reference
updated 8.9 years ago by
gzl
▴ 20 • written 12.6 years ago by
pmuench
▴ 140
0
votes
2
replies
2.2k
views
First steps Hmmer
alignment
hmmer
genome
sequence
updated 8.9 years ago by
Biostar
20 • written 9.0 years ago by
mayegidio
• 0
4
votes
4
replies
2.3k
views
Secondary structure prediction correctness meassure
sequence
secondary structure
prediction
updated 8.9 years ago by
Erik Wright
▴ 420 • written 8.9 years ago by
henry slade
▴ 80
8
votes
8
replies
9.9k
views
Why There Are 3 Fastq File In This Pair-End Data?
paired-end
solid
barcode
updated 2.7 years ago by
Ram
45k • written 13.5 years ago by
Hanfei Sun
▴ 60
2
votes
1
reply
4.6k
views
List of genome sequencing projects
DNA-seq
genome
ngs
sequencing
illumina
8.9 years ago by
cmo
▴ 90
0
votes
3
replies
2.0k
views
optimum number of short reads for denovo assembly
Assembly
updated 8.9 years ago by
dbrowne.up
▴ 80 • written 8.9 years ago by
ebrahimiet
▴ 50
0
votes
2
replies
1.9k
views
Denovo Assemly of unmapped reads
Assembly
updated 8.9 years ago by
dbrowne.up
▴ 80 • written 8.9 years ago by
sukesh1411
▴ 30
3
votes
4
replies
2.0k
views
scoffold level assembly
Assembly
next-gen
updated 8.9 years ago by
dbrowne.up
▴ 80 • written 8.9 years ago by
reza
▴ 300
3
votes
2
replies
4.2k
views
estimate genome coverage
masurca
kmergenie
Assembly
updated 8.9 years ago by
dbrowne.up
▴ 80 • written 8.9 years ago by
Ric
▴ 440
0
votes
2
replies
2.9k
views
how to assign kmer value for paired end reads
Assembly
updated 8.9 years ago by
dbrowne.up
▴ 80 • written 8.9 years ago by
girijakaushal
▴ 10
1
vote
5
replies
3.2k
views
Heatmap from chromosome co-ordinates
Heatmap
Chromosome
Coordinate
Ideogram
R
updated 8.9 years ago by
mforde84
★ 1.4k • written 8.9 years ago by
caspase8mach
▴ 30
7
votes
4
replies
5.6k
views
Forum:
microbiology or bioinformatics?
decision
updated 2.3 years ago by
Ram
45k • written 8.9 years ago by
sammykrom
• 0
2
votes
1
reply
2.4k
views
geo2r to replicate publication results
geo2r
geo
ncbi
updated 8.9 years ago by
TriS
★ 4.8k • written 8.9 years ago by
jiwpark00
▴ 230
0
votes
2
replies
1.5k
views
bar code manipulation
bar code
updated 8.9 years ago by
Amitm
★ 2.3k • written 8.9 years ago by
rob.costa1234
▴ 310
2
votes
2
replies
1.5k
views
CAR parameters not work
Assembly
updated 8.9 years ago by
Sej Modha
5.3k • written 8.9 years ago by
Giffredo
▴ 10
6
votes
12
replies
5.8k
views
Reading .sam files in java
sequencing
next-gen
java
sam
Picard
updated 8.9 years ago by
Pierre Lindenbaum
166k • written 8.9 years ago by
torkel.loman
▴ 10
2
votes
5
replies
11k
views
Downloaing SRA using Aspera
SRS
NCBI
ASPERA
8.9 years ago by
always_learning
★ 1.2k
1
vote
2
replies
3.5k
views
Ucsc Whole Genome Pairwise Alignment
updated 8.9 years ago by
Biostar
20 • written 11.3 years ago by
masih.mahmoudi
• 0
5
votes
2
replies
5.1k
views
NCBI Blast locally: filter by accession number and NOT by GI number
ncbi
updated 8.9 years ago by
GenoMax
152k • written 8.9 years ago by
tlorin
▴ 370
0
votes
0
replies
2.3k
views
Dispersion estimates DESeq2
Dispersion estimates DESeq
8.9 years ago by
javiergutierreza
▴ 40
0
votes
5
replies
2.9k
views
How to calculate fraction of RNA-Seq reads mapped to a customised genomic locations?
RNA-Seq
updated 8.9 years ago by
WouterDeCoster
48k • written 8.9 years ago by
biorepine
★ 1.5k
1
vote
2
replies
4.6k
views
SPAdes insert size
SPAdes
genome
miseq
8.9 years ago by
treitlis
▴ 40
4
votes
10
replies
2.3k
views
How long does it take to get a License for Desmond software?
Desmond
License
8.9 years ago by
kolyadenkoilya94
• 0
1
vote
2
replies
2.9k
views
Error in SAMseq analysis with R
r
RNA-Seq
8.9 years ago by
namilio06
▴ 10
4
votes
2
replies
2.7k
views
Getting fasta sequence of significant transcripts/genes after cuffdiff
RNA-Seq
cuffdiff
cufflink
fasts
updated 8.9 years ago by
i.sudbery
21k • written 8.9 years ago by
dasdevashishdas
▴ 120
8
votes
13
replies
3.8k
views
Number of reads in one gene affect the differential expression analysis?
RNA-Seq
DESeq
counts
DEG
RNASeq
updated 8.9 years ago by
i.sudbery
21k • written 8.9 years ago by
camelbbs
▴ 710
1
vote
1
reply
2.4k
views
Should I run Gap close in assembly ?
gap close
updated 8.9 years ago by
Medhat
9.8k • written 9.0 years ago by
Picasa
▴ 690
14
votes
2
replies
14k
views
Picard vs Samtools duplicate removal
sequencing
alignment
next-gen
Assembly
updated 8.9 years ago by
i.sudbery
21k • written 8.9 years ago by
conorproud89
▴ 20
1
vote
4
replies
3.4k
views
IGV Visualisation Problem
IGV
VCF
snpsift
vcftools
8.9 years ago by
morovatunc
▴ 560
0
votes
1
reply
1.8k
views
visualize noncoding mutations
cbioportal
cancer
genome
8.9 years ago by
Pappu
★ 2.1k
1
vote
0
replies
2.0k
views
Consensus from mpileup error
genome
sequencing
alignment
SNP
8.9 years ago by
mks002
▴ 220
0
votes
1
reply
1.9k
views
CrossMap issues changing genome version
RNA-Seq
ChIP-Seq
software error
updated 3.7 years ago by
ellenbdrake30
• 0 • written 8.9 years ago by
Satyajeet Khare
★ 1.6k
0
votes
1
reply
1.6k
views
How to find all chloroplast genes from SNP data of whole genome of 200 rice accession??
gene
SNP
genome
8.9 years ago by
naveedkhanchemist
• 0
2
votes
7
replies
5.8k
views
How can I upgrade bowtie2-2.2.6 to bowtie2-2.2.9 or uninstall this old version?
bowtie2-2.2.9
centos server
uninstall
updated 8.9 years ago by
JackieMe
▴ 30 • written 8.9 years ago by
mirza
▴ 180
2
votes
5
replies
1.9k
views
Truncate RNASeq data to get similar abundance
rnaseq
8.9 years ago by
camelbbs
▴ 710
2
votes
3
replies
5.1k
views
questions about rMATS output
RNA-Seq
updated 8.9 years ago by
Charles Warden
8.3k • written 8.9 years ago by
zhaopeihua0520
▴ 10
0
votes
2
replies
2.1k
views
Cufflinks version higher than 1.3.0 gives 0 DEG
RNA-Seq
updated 2.9 years ago by
Ram
45k • written 9.5 years ago by
debashis.bioinfo
• 0
1
vote
2
replies
3.6k
views
Why it is important to remove duplicate sequences before a ML tree construction?
viral evolution analysis
Tree construction
gene
updated 2.5 years ago by
Greg P
▴ 70 • written 8.9 years ago by
armando.torre
▴ 10
0
votes
0
replies
1.4k
views
Biological Meaning for the Structure Figure in String 9.0
string
pathway
interaction
8.9 years ago by
Shicheng Guo
★ 9.6k
121,546 results • Page
1784 of 2431
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Comment: Draw GO tree for some GO ids with coloring
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C: How should I handle the raw reads with failed per base sequence content in fastQ
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Recent Replies
Answer: How to extract gene list from GEO dataset in R
by
Muhammad
• 0
Hi I saw the GSE239903 dataset. It contains RNAseq data along with ATACseq data. To get the gene IDs you can follow the scRNA seq pipeline …
Answer: RNA seq strandedness (reverse-strand)
by
Muhammad
• 0
Hi, you can use hisat2 for alignment then Sam tools and then featurecount for coun matrix... Hisat2 code is hisat2 -x genome_index -1 read…
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
by
dariober
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
jared.andrews07
★ 19k
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
michael.ante
★ 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…
Comment: calculating coverage of gene in my metagenomes with samtools
by
Pierre Lindenbaum
166k
if you use the same filtering and `samtools depth -a ` there should be no difference isn't it ? samtools coverage would be faster.
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