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1,000 results • Page
2 of 20
Sort: replies
Rank
Views
Votes
Replies
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 23 days ago by
Ram
43k • written 5.5 years ago by
c.clarido
▴ 110
7
votes
12
replies
1.6k
views
How to pass arguments in a bash script to perform read alignment to the reference?
exome
bwa
bash
updated 5 months ago by
Ram
43k • written 4.2 years ago by
Karma
▴ 310
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
4
votes
12
replies
7.7k
views
6 follow
BWA error: no ID within the read group line
bwa
readgroups
RG
parallel
updated 10 weeks ago by
mgdrnl
▴ 10 • written 3.3 years ago by
whb
▴ 60
2
votes
12
replies
1.7k
views
gatk Funcotator
vcf
Funcotator
gatk
9 months ago by
Saurabh
• 0
3
votes
12
replies
473
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
16 days ago by
Lila M
★ 1.2k
2
votes
12
replies
1.5k
views
scrna seq analysis - doublets
scrna
seq
code
r
updated 9 months ago by
Nitin Narwade
★ 1.6k • written 9 months ago by
bioinformatics
▴ 40
5
votes
11
replies
986
views
Make heatmap for RNA-seq with non replicate
RNA-seq
updated 8 months ago by
Ram
43k • written 8 months ago by
Chris
▴ 260
0
votes
11
replies
2.2k
views
i want to convert .ht2 files into FASTA file
GATK
HISAT2
FASTA
updated 10 months ago by
Ram
43k • written 4.9 years ago by
saumya.sharma1509
• 0
0
votes
11
replies
770
views
Filtering VCF based on codon-transcript
vcf
bcftools
updated 4 weeks ago by
barslmn
★ 2.1k • written 6 weeks ago by
avelarbio46
▴ 30
4
votes
11
replies
1.7k
views
PCA WITH PLINK
PLINK
updated 8 months ago by
Kevin Blighe
87k • written 8 months ago by
Michelle Guerra
• 0
2
votes
11
replies
1.0k
views
Data preparation for a ML model
machine-learning
RNA-Seq
R
python
biomarkers
4 months ago by
sil_bioinfo
▴ 40
2
votes
11
replies
5.2k
views
How long it takes to run repeat masker on a full genome
Assembly
updated 3 months ago by
e.r.zakiev
▴ 190 • written 7.8 years ago by
CAnna
▴ 20
5
votes
11
replies
1.3k
views
Interpret IGV output inversion
variant-calling
IGV
alignment
updated 8 months ago by
cmdcolin
★ 3.8k • written 8 months ago by
pablo
▴ 300
2
votes
11
replies
729
views
Reference Guided genome assembly
tabix
updated 7 weeks ago by
Michael
54k • written 8 weeks ago by
sainavyav22
• 0
4
votes
11
replies
606
views
Remove X in row name with only number
GSVA
updated 10 weeks ago by
Ram
43k • written 10 weeks ago by
Chris
▴ 260
4
votes
11
replies
1.6k
views
Check Strandedness
Check_Strandedness
how_are_we_stranded_here
leafcutter
bash
updated 6 months ago by
Brian Bushnell
20k • written 8 months ago by
Y
• 0
0
votes
11
replies
1.6k
views
count file having zero
RNA-Seq
next-gen
alignment
updated 10 months ago by
Ram
43k • written 5.2 years ago by
BioBaby
▴ 20
0
votes
11
replies
1.1k
views
Normalization for microarrays >1000+ samples?
microarray
normalization
oligo
7 months ago by
evmae
• 0
1
vote
11
replies
1.2k
views
Quantification after transcriptome assembly with Trinity
De-novo-transcriptome-assembly
Trinity
RNA-seq-analysis
updated 6 months ago by
GenoMax
141k • written 7 months ago by
langziv
▴ 50
1
vote
10
replies
964
views
file conversion from gtf to gff3 for evidence modeler
gff3
stringtie
gtf
6 months ago by
rj.rezwan
• 0
14
votes
10
replies
881
views
How to remove center population from seurat cluster
single-cell
4 months ago by
synat.keam
▴ 100
8
votes
10
replies
2.0k
views
PyWGCNA
WGCNA
10 months ago by
yoshifumimiya
▴ 40
3
votes
10
replies
1.2k
views
STAR index not working
STAR
RNA-Seq
7 months ago by
camillab.
▴ 160
1
vote
10
replies
1.1k
views
Do monoclonal antibodies have a blocking effect?
block
antibody
offtopic
updated 8 months ago by
Jeremy
▴ 880 • written 8 months ago by
jinyu
▴ 10
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
8
votes
10
replies
658
views
bash script
whole-genome-sequencing
updated 3 days ago by
Ram
43k • written 10 days ago by
bestone
▴ 30
2
votes
10
replies
788
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 21 days ago by
Ram
43k • written 8 weeks ago by
Sky
▴ 10
5
votes
10
replies
1.2k
views
the distribution of log2Fc and t value are not similar for bulk RNA-seq
decoupleR
RNA-seq
7 months ago by
alwayshope
▴ 40
0
votes
10
replies
922
views
ONT Raw Read Sequencing Pipeline
remora
dorado
ONT
Basecall
3 months ago by
turcoa1
• 0
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 1 day ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
1
vote
10
replies
1.7k
views
Deepvariant variant calling by singularity
deepvariant
singularity
conda
docker
updated 6 months ago by
jeffhsu3
• 0 • written 9 months ago by
fra.r.silvestro
▴ 10
5
votes
10
replies
836
views
Error when viewing a bam file
samtools
updated 10 months ago by
Ram
43k • written 11 months ago by
Chris
▴ 260
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
0
votes
10
replies
586
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
18 days ago by
dzisis1986
▴ 70
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
1
vote
10
replies
1.2k
views
Coverage histogram query
Alignment
7 months ago by
prasundutta87
▴ 660
0
votes
10
replies
843
views
Problem running scPred
scPred
scPredict
updated 5 weeks ago by
Ram
43k • written 3 months ago by
Nitin
• 0
1
vote
9
replies
1.3k
views
Couldn't get a file descriptor referring to the console multiqc
multiqc
updated 11 months ago by
Ram
43k • written 21 months ago by
smithkthedale
▴ 10
0
votes
9
replies
1.7k
views
WCGNA to Cytoscape
wgcna
cytoscape
rna-seq
updated 10 weeks ago by
Ram
43k • written 3.7 years ago by
ovariohisterectomia
▴ 40
1
vote
9
replies
508
views
miRNA alignment with Bowtie2
bowtie2
4 weeks ago by
Chironex
▴ 40
0
votes
9
replies
1.4k
views
Samtools sam to bam error
samtools
updated 5 months ago by
Andrea
• 0 • written 24 months ago by
kb_93
▴ 10
3
votes
9
replies
667
views
STARsolo seg fault without readMapNumber flag
STAR
RNA-seq
STARsolo
Velocyto
updated 5 months ago by
Ram
43k • written 5 months ago by
rbronste
▴ 420
6
votes
9
replies
2.0k
views
Error when runing Bowtie2: (ERR): bowtie2-align exited with value 1
BAM
Bowtie
updated 11 months ago by
Ram
43k • written 14 months ago by
luzglongoria
▴ 50
3
votes
9
replies
1.7k
views
How to get negative training set if I don't know what constitutes negative?
machine-learning
dna-sequence
blast
updated 5 months ago by
Ram
43k • written 7.6 years ago by
nafizh
• 0
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
1
vote
9
replies
844
views
Python3 or Ubuntu, not perl: Have Primers with Degenerate Bases, Need tool or way to List all Possible Nucleotide Sequences
degenerate-bases
python
primers
biopython
updated 5 weeks ago by
Dave Carlson
★ 1.7k • written 5 weeks ago by
Matthew
• 0
1
vote
9
replies
636
views
Htseq-count reads with missing mate encountered
htseq
htseq-count
5 months ago by
Bjorn
• 0
2
votes
9
replies
7.5k
views
6 follow
Read MAP and PED files in PLINK
GWAS
PLINK
updated 3 months ago by
GenoMax
141k • written 6.0 years ago by
ft821525
• 0
4
votes
9
replies
2.6k
views
Blast+ remote database names
blast
remote
databases
Blastplus
updated 9 months ago by
GenoMax
141k • written 2.3 years ago by
Komalharini
• 0
1,000 results • Page
2 of 20
Recent Votes
Comment: SLURM submission problem: Indexing the Reference Genome is not done in STAR
Answer: Indexing the Reference Genome is not done in STAR
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
Comment: Filtration Of Reads With Length Lower Than 30 From Bam
How to compare the quality of assemblies
Filtration Of Reads With Length Lower Than 30 From Bam
Answer: Filtration Of Reads With Length Lower Than 30 From Bam
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Recent Replies
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
▴ 500
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…
Comment: RNA seq differential expression analysis
by
swbarnes2
14k
No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
Answer: Adding CB tag to bam file
by
swbarnes2
14k
Shouldn't you use PicardTools for this?
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
Sure. Or, one could do: bash try.bash "Homo sapiens" AHR | xargs -I v_pdb curl -s -o v_pdb.pdb https://files.rcsb.org/view/v_pdb.pdb
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