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42 results • Page
1 of 1
Sort: Rank
Rank
Views
Votes
Replies
0
votes
2
replies
54
views
Miseq mothur error with SOP in galaxy - Help please!
mothur
miseq
16s
Galaxy
sop
updated just now by
colindaven
4.4k • written 3 hours ago by
Melissa
• 0
0
votes
1
reply
40
views
Find corresponding branch from gene tree in species tree
phylogeny
family-tree
gene
species
phylogenetics
updated 50 minutes ago by
Ram
38k • written 2 hours ago by
Charlotte West
▴ 40
0
votes
2
replies
74
views
How can I creating multisample VCF file ?
VCF
updated 48 minutes ago by
Ram
38k • written 4 hours ago by
eennadi
▴ 20
0
votes
0
replies
54
views
How to identify the batch informations from the sample ID?
batch-correction
TCGAbatch
DESeq2
TCGA
updated 39 minutes ago by
Ram
38k • written 5 hours ago by
dare_devil
★ 1.7k
0
votes
1
reply
57
views
Adaptor sequences in GIAB samples
illumina
GIAB
adaptor
cutadapt
updated 4 hours ago by
GenoMax
125k • written 5 hours ago by
Mk
▴ 10
0
votes
3
replies
97
views
pileup consolidation tool
RNAseq
pileup
jacusa
samtools
6 hours ago by
joe
▴ 380
0
votes
2
replies
138
views
How I know the genome assembly quality by the low coverage Pacbio data ?
genome
Pacbio
6 hours ago by
wdpang
• 0
0
votes
0
replies
65
views
Stringtie prepDE.py script
deseq2
stringtie
updated 41 minutes ago by
Ram
38k • written 13 hours ago by
Aiswarya
• 0
0
votes
2
replies
101
views
Averaging across multiple proteomic experiments
statistics
proteomics
R
updated 1 hour ago by
ATpoint
68k • written 13 hours ago by
bhumm
▴ 20
0
votes
2
replies
128
views
Copy Number Variants, where to start?
CNV
annotation
41 minutes ago by
paolo
▴ 60
0
votes
0
replies
76
views
mosdepth coverage & transcripts per million
TPM
coverage
metagenome
mosdepth
16 hours ago by
hannahf
• 0
0
votes
2
replies
123
views
FATAL: While performing build: build image size <= 0 - Issues With Singularity
R
Docker
Singularity
1 hour ago by
Indira
• 0
0
votes
1
reply
102
views
Methods for downsampling coverage in a VCF
BCFTools
downsampling
WGS
sequencing
GATK
updated 16 hours ago by
Medhat
9.5k • written 16 hours ago by
a
• 0
0
votes
0
replies
79
views
Questions about HVGs and HEGs in single cell research
single-cell
machine-learning
updated 17 hours ago by
Ram
38k • written 18 hours ago by
me
• 0
0
votes
0
replies
73
views
average expression function and pct
seurat
average
pct
expression
and
19 hours ago by
rasing02
• 0
0
votes
0
replies
80
views
GoSemSIm - function mgeneSim() is resulting in similarity matrix without 1s od diagonal
vs
Gosim
GoSemSIm
20 hours ago by
eliska.ochodkova
• 0
0
votes
2
replies
148
views
Error with FindConservedMarkers()
FindConservedMarkers
20 hours ago by
Chris
▴ 60
0
votes
0
replies
88
views
Extract different variants of a vcf file comparing to other vcf files
gatk
bedtools
mutect2
vcftools
variant
3 hours ago by
minoo
▴ 10
0
votes
3
replies
192
views
BWA-mem not working with Snakemake + singularity
snakemake
bwa
singularity
updated 22 hours ago by
Jeremy Leipzig
21k • written 1 day ago by
brunobsouzaa
▴ 800
0
votes
0
replies
102
views
Using bigWigCompare to correct for input signal
chip
input
peaks
bigwig
deeptools
21 hours ago by
Maycon
• 0
1
vote
4
replies
371
views
SNP calling
SNP
GATK
updated 4 hours ago by
dthorbur
▴ 270 • written 4 days ago by
abozorgmehr1985
▴ 10
0
votes
2
replies
208
views
merging and annotating bcf files for variant calling
vcf
bcf
bcftools
variant-calling
updated 17 hours ago by
Ram
38k • written 9 days ago by
pr.khavari
• 0
0
votes
3
replies
326
views
promoter analysis in plant
GAD
plantCARE
script
python
result
23 hours ago by
Nelo
• 0
0
votes
5
replies
4.3k
views
Error during Trinity running with the recent version?
next-gen
Assembly
RNA-Seq
updated 22 hours ago by
Ram
38k • written 7.8 years ago by
seta
★ 1.7k
0
votes
0
replies
2.6k
views
converting vcf to gds losing some snps
gds
vcf
updated 18 hours ago by
Ram
38k • written 7.8 years ago by
gulcek
▴ 20
0
votes
0
replies
2.1k
views
SNPSift - Token Recognition Error
snpsift
java
updated 21 minutes ago by
Ram
38k • written 7.8 years ago by
anon123
▴ 10
2
votes
0
replies
2.4k
views
How to start a SNP prioritization in GWAS
gwas
snp-prioritization
updated 17 hours ago by
Ram
38k • written 7.8 years ago by
kumar.vinod81
▴ 330
2
votes
1
reply
7.5k
views
ROH by PLINK
ROH
plink
updated 17 minutes ago by
Ram
38k • written 7.8 years ago by
afadda
▴ 20
0
votes
5
replies
2.9k
views
Short homopolymer runs overrepresented at 3' ends of R2 Illumina RNAseq reads, breaking tophat alignment
RNA-Seq
QC
updated 16 hours ago by
Ram
38k • written 7.9 years ago by
ethan.kaufman
▴ 380
1
vote
0
replies
1.7k
views
Counting features - the example in vignette for summarizeOverlap and HTseq
RNA-Seq
updated 22 hours ago by
Ram
38k • written 7.8 years ago by
Pfs
▴ 550
0
votes
0
replies
4.0k
views
vcftools FORMAT ID error during filtering
vcf
vcftools
updated 22 hours ago by
Ram
38k • written 7.8 years ago by
wickell.david
• 0
0
votes
0
replies
2.1k
views
Extract (assume) related pathway(s) from the list of genes
RNA-Seq
updated 22 hours ago by
Ram
38k • written 7.8 years ago by
fedexsmallbox
• 0
2
votes
1
reply
2.8k
views
EdgeR output normalization?
RNA-Seq
updated 22 hours ago by
Ram
38k • written 7.8 years ago by
mahnazkiani
▴ 50
0
votes
5
replies
2.1k
views
BioPerl: Use of uninitialized value $Bio::DB::NCBIHelper::HOSTBASE
bioperl
perl
updated 21 hours ago by
Ram
38k • written 7.8 years ago by
tino_s3004
• 0
2
votes
0
replies
1.6k
views
Finding appropriate ligand for docking
next-gen
updated 21 hours ago by
Ram
38k • written 7.8 years ago by
mbstuanindya
▴ 20
0
votes
3
replies
1.3k
views
Match trimmed sequences with full length reference set
sequence
dna
updated 21 hours ago by
Ram
38k • written 7.8 years ago by
pmr
• 0
0
votes
0
replies
1.5k
views
Mapmi error, no alignments found.
MapMi
Dust
updated 18 hours ago by
Ram
38k • written 7.8 years ago by
The Last Word
▴ 230
2
votes
0
replies
2.1k
views
Four Gamete Test
four-gamete-test
updated 18 hours ago by
Ram
38k • written 7.8 years ago by
thakurshalabh
▴ 60
0
votes
4
replies
1.3k
views
subsetting sets of scaffolds based on sequence similarity
sam
NGS
bam
Assembly
updated 16 hours ago by
Ram
38k • written 7.8 years ago by
ramesh.8v
▴ 210
1
vote
1
reply
2.1k
views
Identifying Non Synonymous mutations in bacterial genomes
SNP
R
next-gen
genome
sequence
updated 17 hours ago by
Ram
38k • written 7.8 years ago by
mmart12
▴ 30
0
votes
2
replies
2.5k
views
program to pull out 5'and 3'utr from cds file
utr
cds
updated 18 hours ago by
Ram
38k • written 7.9 years ago by
vigneshprbh37
▴ 30
0
votes
1
reply
3.5k
views
Processing OrthoMCL output file, "groups.txt" to create a venn diagram
genome-comparison
OrthoMCL
Core-genome
orthologs
updated 18 hours ago by
Ram
38k • written 7.9 years ago by
jc_0919
• 0
42 results • Page
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Recent Votes
Comment: Bacterial metatranscriptomics with DESEQ2?
C: How to extend contigs from single-end reads?
C: How to extend contigs from single-end reads?
Answer: Seurat or Bioconductor for single cell RNA seq
Seurat or Bioconductor for single cell RNA seq
Answer: Seurat or Bioconductor for single cell RNA seq
Answer: Seurat or Bioconductor for single cell RNA seq
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Recent Awards •
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mathavanbioinfo
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Recent Replies
Comment: Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
by
Ram
38k
Do not add answers unless you're **answering** the top level question. Use `Add Comment` or `Add Reply` instead as appropriate. I've moved …
Answer: Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
by
BioinfoBee
• 0
@juke34 I tried the agat_sp_gxf_to_gff3.pl to sort the gff3 by their chromosome order but doesn't seems to work. Any suggestions?.
Comment: CNV Prediction Tools
by
Quentin M
▴ 60
Give a try to [CODEX2][1] [1]: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1578-y
Comment: Problem with tximport and plasmodium falciparum
by
bioinfo
▴ 20
Thank you. It does not seem to be that. I changed my script a bit. Now it looks like shown below: mart <- biomaRt::useMart("protists_…
Comment: Copy Number Variants, where to start?
by
paolo
▴ 60
I have found autoCNV, inCNV, and ClassifyCNV. The second one is for exomic CNVs only, and the third one does not run on Windows, but it mig…
Comment: BLAST reference genome indexing
by
GenoMax
125k
That is correct.
Comment: BLAST reference genome indexing
by
bhumm
▴ 20
Thanks for the explanation and links. So when calling the database in the for use, I call the prefix of all the 'subfiles' which invokes th…
Comment: Averaging across multiple proteomic experiments
by
bhumm
▴ 20
It is two biological replicates. I reasoned it as increasing N=2. For both biological replicates, it is ~13 controls vs ~13 disease conditi…
Comment: How to summarize the expression of a gene when having expression data from diffe
by
i.sudbery
16k
tximport will calculate the weighted effective transcript length, but it doesn't use that in its calculation of gene level expression. Both…
Comment: FATAL: While performing build: build image size <= 0 - Issues With Singularity
by
Indira
• 0
I was building a docker image I created on my computer on an HPC. It seems that due to some network issues I kept getting this FATAL messag…
Answer: Seurat or Bioconductor for single cell RNA seq
by
Lindsey
▴ 10
Seurat is an R package, so if you're used to work with other Bioconductor packages, you should be fine! Also the tutorials and manuals from…
Answer: Seurat or Bioconductor for single cell RNA seq
by
Basti
★ 1.3k
Bioconductor is a package repository so your question is not accurate. Maybe you hesitate between Seurat and other packages dedicated to sc…
Answer: fastq-dump split-spot and skip-technical
by
Larissa Graciano
• 0
The link to the blog post isn't working, I believe this is the updated one: https://edwards.flinders.edu.au/fastq-dump/
Comment: Find corresponding branch from gene tree in species tree
by
andres.firrincieli
3.1k
check Notung: [link][1] [1]: http://www.cs.cmu.edu/~durand/Notung/
Comment: Help please! Miseq SOP with galaxy toolsuite
by
Melissa
• 0
I have posted in their forum but I have not found a solution yet. I was posting here for an alternative help source. I am running mother…
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