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1,000 results • Page
2 of 20
Sort: Views
Rank
Views
Votes
Replies
0
votes
16
replies
3.8k
views
Gff to genbank - feature is missing
DNA
augustus
gff3
genbank
updated 11 months ago by
Ram
43k • written 5.9 years ago by
rororo
▴ 10
0
votes
7
replies
3.7k
views
MUMmer plot visualization
MUMmer plot
updated 8 weeks ago by
Carlos
• 0 • written 3.2 years ago by
rthapa
▴ 90
2
votes
4
replies
3.7k
views
Converting different annotation file formats (GTF/GFF/BED) to each other
rna-seq
next-gen
updated 6 months ago by
alejandrogzi
▴ 120 • written 6.6 years ago by
Javad
▴ 150
10
votes
7
replies
3.7k
views
What is Pathway Analysis?
database
analysis
ontology
pathway
updated 10 months ago by
Ram
43k • written 8.0 years ago by
Pranavathiyani G
▴ 330
2
votes
4
replies
3.7k
views
6 follow
Gene correlation with single cell data?
RNA-Seq
gene
updated 3 months ago by
Quang
• 0 • written 3.1 years ago by
theodore.killian
▴ 30
5
votes
8
replies
3.6k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 9 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
5
votes
35
replies
3.6k
views
Reduce set of chromosomes in Pangenome graph
pangenome
vg
updated 9 months ago by
Jordan M Eizenga
▴ 460 • written 10 months ago by
anivlete
• 0
1
vote
2
replies
3.5k
views
rna-seq analysis with Salmon - how to Import and summarize using tximport
RNA-Seq
salmon
tximport
updated 6 months ago by
camillab.
▴ 160 • written 4.6 years ago by
woojoy14
▴ 10
4
votes
12
replies
3.5k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling
samtools
VCF
BCF
updated 24 days ago by
Ram
43k • written 5.5 years ago by
c.clarido
▴ 110
0
votes
2
replies
3.5k
views
dN/dS ratio from .vcf file
synonmous
non-synomous
mutation
updated 6 months ago by
rohitsatyam102
▴ 840 • written 5.4 years ago by
shubhra.bhattacharya
▴ 140
4
votes
8
replies
3.5k
views
How to reduce the number of SNPs for the Lositan software
Lositan
SNP
updated 9 months ago by
Ram
43k • written 9.5 years ago by
zhaojianli198322
• 0
3
votes
4
replies
3.4k
views
any recommended tools for batch effect and normalization not written in R?
R
RNA-Seq
combat
python
batch-effect
updated 19 hours ago by
Ram
43k • written 7.1 years ago by
dyollluap
▴ 310
1
vote
8
replies
3.4k
views
Best way to address different batches of RNA-seq
sequence
RNA-Seq
RPKM
Fold-Change
batch-effect
updated 1 day ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 2 days ago by
Ram
43k • written 7.4 years ago by
linda
• 0
3
votes
4
replies
3.4k
views
Switch ref/alt alleles vcf file
SNP
vcf
sequencing
updated 3 months ago by
jvt
• 0 • written 4.4 years ago by
mdstep
▴ 20
1
vote
1
reply
3.4k
views
Problem with PGDSpider v 2.1.0.2
alignment
updated 10 months ago by
sackettl
▴ 20 • written 7.8 years ago by
maria.segovia.ramirez
▴ 10
1
vote
2
replies
3.4k
views
How to convert FASTA to NEXUS in Python
fasta
biopython
nexus
updated 9 months ago by
Ram
43k • written 3.7 years ago by
adrian18_07
▴ 10
0
votes
0
replies
3.4k
views
Find conserved blocks and extract subalignment with Python
multiple-sequence-alignment
python
updated 11 months ago by
Ram
43k • written 7.0 years ago by
Kevin D
▴ 30
0
votes
4
replies
3.4k
views
Polyploidy found, and not supported by vcftools
SNP
updated 10 months ago by
Ram
43k • written 5.2 years ago by
sambioinfo2018
▴ 20
1
vote
14
replies
3.3k
views
How to convert Haplotypes file to PLINK format data
R
plink
updated 11 months ago by
Ram
43k • written 5.9 years ago by
bha
▴ 80
2
votes
12
replies
3.3k
views
WCGNA installation help
R
WGCNA
updated 10 weeks ago by
Ram
43k • written 4.9 years ago by
prekrish
• 0
1
vote
6
replies
3.3k
views
Filter VCF file
snp
next-gen
updated 9 months ago by
Ram
43k • written 7.8 years ago by
sukesh1411
▴ 30
0
votes
12
replies
3.3k
views
comparative analysis of two strains of bacteria's genomes
genome
gene
updated 11 months ago by
Ram
43k • written 6.5 years ago by
fonteneaudam
▴ 20
1
vote
9
replies
3.3k
views
build databses for genome using snpEff
annotation
SNP
snpEff
updated 8 months ago by
nehakhilwani18
• 0 • written 5.7 years ago by
StudentBio
• 0
4
votes
4
replies
3.3k
views
Unable to install Autogrid4
autogrid
software-error
autogrid4
updated 11 months ago by
Ram
43k • written 3.1 years ago by
roybatty269
• 0
0
votes
1
reply
3.3k
views
Cutadapt 1.9.1 error
cutadapt
next-gen
updated 10 months ago by
Ram
43k • written 8.2 years ago by
vishweshwaransridhar
▴ 10
2
votes
5
replies
3.2k
views
How to output colored alignment from clustal omega stand alone tool?
Clustal Omega
Colored alignment
updated 8 months ago by
Joe
21k • written 4.7 years ago by
MB
▴ 50
20
votes
17
replies
3.2k
views
How to add "transcript" feature to a gtf file?
gtf
updated 9 months ago by
1769mkc
★ 1.2k • written 3.2 years ago by
pomodoro_sinensis
▴ 110
3
votes
7
replies
3.2k
views
vcf filter for FORMAT argument (DP/GQ/GQX > 30) multiple (380) vcf file
vcffilter
vcftools
sequencing
updated 9 months ago by
Ram
43k • written 4.1 years ago by
IndyDNA
▴ 10
0
votes
1
reply
3.2k
views
How to convert g.vcf to .vcf file
vcf
sequence
genome
alignment
updated 10 months ago by
Ram
43k • written 5.0 years ago by
Sakhaa
• 0
2
votes
10
replies
3.2k
views
6 follow
Split plink files by a number of SNPs
GWAS
SNP
plink
updated 6 months ago by
Raygozak
★ 1.4k • written 5.8 years ago by
kakukeshi
▴ 80
3
votes
5
replies
3.2k
views
GO annotation for rice in an R package
annotation
R
updated 12 weeks ago by
prity6459
• 0 • written 7.4 years ago by
djyjin
▴ 10
6
votes
6
replies
3.2k
views
ChIP-Seq Intensity Analysis
R
ChIP-Seq
updated 11 months ago by
Ram
43k • written 6.4 years ago by
solveforj
▴ 20
5
votes
7
replies
3.1k
views
8 follow
bwa mem -T (alignment score) not doing anything
SNP
genome
sequence
updated 6 months ago by
Istvan Albert
100k • written 5.9 years ago by
chris.bird
▴ 10
0
votes
1
reply
3.1k
views
PSMC plot (Effective population size)
next-gen
updated 7 months ago by
1601693223
• 0 • written 8.4 years ago by
vicky
▴ 30
3
votes
6
replies
3.1k
views
samtools sort not working when using multiple threads
samtools
bam
updated 10 months ago by
Ram
43k • written 2.2 years ago by
bio_elle
▴ 10
1
vote
7
replies
3.1k
views
RGT TypeError: unsupported operand type(s) for +: 'NoneType' and 'int'
RGT
TF-footprinting
ATAC-seq
updated 10 months ago by
Ram
43k • written 5.4 years ago by
grant.hovhannisyan
★ 2.6k
1
vote
10
replies
3.1k
views
How to specify/calculate subject coverage of the alignment (alignment of query[protein sequence] and subject[Nucleotide sequence]) in tBLASTn?
alignment
BLAST
tBLASTn
updated 10 months ago by
Ram
43k • written 5.1 years ago by
Kumar
▴ 120
0
votes
7
replies
3.1k
views
How much time should be expected for building a database by kraken2-build?
kraken2
updated 11 months ago by
Ram
43k • written 3.2 years ago by
thitrucminh.nguyen
• 0
0
votes
3
replies
3.1k
views
From FASTQ to clean BAM using GATK tutorial #6484
gatk
MergeBamAlignment
uBAM
bamclipper
updated 11 months ago by
Ram
43k • written 6.5 years ago by
lamteva.vera
▴ 220
0
votes
3
replies
3.0k
views
Rna-seq for differential expression analysis
differential-expression
transcriptome
updated 19 hours ago by
Ram
43k • written 8.9 years ago by
siddharth.patel.153
• 0
2
votes
6
replies
3.0k
views
hisat2 :Killed (ERR): hisat2-align exited with value 137
RNA-seq
alignment
hisat2
updated 7 months ago by
Ram
43k • written 2.3 years ago by
iamsmor
• 0
3
votes
6
replies
3.0k
views
Which of the 4 SureSelect Agilent BED files to use with GATK haplotype caller?
gatk
variant calling
sureselect
updated 8 months ago by
LeandroF.
• 0 • written 4.2 years ago by
curious
▴ 750
3
votes
12
replies
3.0k
views
What is NCBI Gene ID, where to find it and how to convert to entrez ID?
RNA-Seq
updated 10 months ago by
Pegasus
▴ 100 • written 4.5 years ago by
mnazir
▴ 10
1
vote
5
replies
3.0k
views
Problem in running NOISeq-sim
NOISeq
RNA-Seq
updated 10 months ago by
Ram
43k • written 5.7 years ago by
jaspreetk.dhanjal
▴ 20
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq
batch-effect
sequencing
updated 19 hours ago by
Ram
43k • written 6.9 years ago by
endikavarela
• 0
0
votes
2
replies
3.0k
views
How to convert gbk file to roary tool acceptable gff3 format?
linux
bash
python
perl
updated 10 months ago by
Ram
43k • written 3.6 years ago by
Kumar
▴ 120
0
votes
1
reply
2.9k
views
RNA-seq compare FPKM's or fold change of different organisms
gene-expression
FPKM
RNA-seq
fold-change
updated 7 months ago by
Ram
43k • written 6.7 years ago by
jehu
▴ 30
1
vote
4
replies
2.9k
views
DBD::mysql::st execute failed: The table 'InplgOrthoInplg
orthomcl
ortho
ubuntu
mysql
updated 11 months ago by
Ram
43k • written 5.8 years ago by
wocana
▴ 20
6
votes
9
replies
2.9k
views
How to analyze the scRNA seq Fastq files from NCBI
SRAtool
Cellranger
NCBI
updated 10 months ago by
Ram
43k • written 2.3 years ago by
aimanbarki
▴ 20
1,000 results • Page
2 of 20
Recent Votes
How To Generate Phylogeny Tree, Based On Snps?
How To Construct Phylogenetic Tree Using Snps
Basic normalization, batch correction and visualization of RNA-seq data
A: Read counts of STAR with gff file
Comment: Free/open source 23andme-like analysis
A: How to obtain all accession.version identifiers for a BLAST database using ENTRE
Comment: Editing Human Reference Genome by adding a CDS
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Answer: Memory usage of picard Samsort
by
tamas.malkocs
• 0
For me, setting `TMP_DIR` (`--TMP_DIR /home/tmp`) didn't work in picard 2.21.1. What solved the issue was setting the environmental variabl…
Answer: Plink merge errors.
by
Dinmukhamed
• 0
I found answer https://www.biostars.org/p/101191/.
Comment: Ciriquant not configuring hisat2 indexed files
by
Atul K.
• 0
it worked. Thank you. Now my terminal is crashing, seems 16gb of RAM and 4 cores isn't enough. Can you suggest something?
Comment: Adding CB tag to bam file
by
Maria
• 0
I checked Picard ```AddOrReplaceReadsGroups``` and ```AddOATag```. Is that what you're referring to?
Comment: Free/open source 23andme-like analysis
by
Michael
54k
Noted that 'accurate' wasn't among your criteria ;) Anyway, most variant callers are free open-source software. However, for ancestry ana…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
by
Pierre Lindenbaum
161k
> server so I cannot use Blat for this purpose. blat is avilable as a standane tool: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
by
b.contreras.moreira
▴ 160
My favourite for this task would be [GMAP]( http://research-pub.gene.com/gmap ), which can produce GFF format with option `-f 2`. It is…
Answer: Prediction of Ribosomal RNA Genes Using RNAmmer Software
by
colindaven
6.3k
Another alternative is the truly free implementation barrnap https://github.com/tseemann/barrnap. This is also installable via conda so qui…
Comment: Filtration Of Reads With Length Lower Than 30 From Bam
by
Hagen
▴ 10
thanks! This saved me quite some time, I was about to write code to calculate the aligned length from the CIGAR. But this can be done with …
Comment: Per base sequence content failed miserably
by
Kai Xin
• 0
will look into that. Thank you very much
Comment: Korean human genome reference file
by
SeoGyun
• 0
Thanks..... But I want to do imputation, so I have to make it as a vcf file, but the site only has a fatsa file....
Comment: miRNAs quantification using mirdeep2 tool
by
Ashok
• 0
thank you for your reply https://github.com/rajewsky-lab/mirdeep2/blob/master/TUTORIAL.md i saw this github tutorial for miRNA quantifica…
Comment: Load a full GFF3 into annotation track using arrow (Apollo)
by
cmdcolin
★ 3.8k
Hi there, I let a developer know of this thread and they said they can check it out next week. Feel free to post to the https://github.com/…
Comment: How to get the reference panel for UKBB
by
航太郎
• 0
Thanks for your guide!
Comment: Removing duplicates
by
joe
▴ 510
I'd try those OP @samuel recommends My guess is you're new to ONT, fast5 is the 'raw data' which is current over time...other than generat…
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