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461 results • Page
2 of 10
Sort: replies
Rank
Views
Votes
Replies
0
votes
4
replies
376
views
Does non-Mendelian equal to mutation?
mutation
genetics
Mendelian
gene
17 days ago by
solarchan7
• 0
2
votes
4
replies
242
views
Retrieve specific fasta sequences from a group of assemblies
CDS
gene
sequence
19 hours ago by
SushiRoll
▴ 100
2
votes
4
replies
185
views
Calculate sequencing file size?
storage
data
sequencing
plan
management
updated 4 days ago by
GenoMax
125k • written 4 days ago by
Lluís R.
★ 1.2k
0
votes
4
replies
2.6k
views
biomaRt: Extracting data for a particular isoform (R/bioconductor)
bioconductor
utr
biomart
updated 6 days ago by
Ram
37k • written 7.7 years ago by
bsmith030465
▴ 210
2
votes
4
replies
331
views
Differences between genomic position and genomic loci?
loci
dna
genome
genetics
gene
21 days ago by
DS
▴ 20
3
votes
4
replies
457
views
Snakemake not executing any tasks
python
readqc
Snakemake
cutadapt
updated 23 days ago by
Jesse
▴ 450 • written 25 days ago by
jaime.alvarez.benayas
▴ 20
0
votes
4
replies
415
views
how to deal with missing genotype data (gt) to do a machine learning
missing_data
updated 21 days ago by
German.M.Demidov
★ 2.9k • written 22 days ago by
arwa.ahmad95
• 0
1
vote
4
replies
411
views
Custom made gff in geneious software - format conversion
format
Geneious
gff
13 days ago by
L_bioinfo
• 0
0
votes
4
replies
690
views
Batch effect correction & normalization after training/test split for gene expression data
RNA-seq
normalization
batcheffect
single_cell_features
training_test_split
updated 1 day ago by
madbadradscientist
▴ 20 • written 5 months ago by
mmitra
▴ 40
5
votes
4
replies
3.4k
views
Black color reads in IGV: bwa-meth
IGV
alignment
bwa-meth
updated 26 days ago by
Ram
37k • written 7.7 years ago by
mehran.karimzade
▴ 220
3
votes
4
replies
462
views
R package DESeq2 in R 3.5.1
packages
installing
error
R
21 days ago by
sehriban.buyukkilic
• 0
0
votes
4
replies
286
views
How to call somatic mutations from vcf files
cancer
vcf
bcf
bam
gene
updated 7 days ago by
Pierre Lindenbaum
152k • written 8 days ago by
DS
▴ 20
0
votes
4
replies
1.4k
views
Automate protein family analysis
protein-family
updated 21 days ago by
Ram
37k • written 7.7 years ago by
biotech
▴ 560
1
vote
4
replies
3.9k
views
design primer for alternative splicing events
alternative-splicing
primer-design
RNA-Seq
updated 10 days ago by
Ram
37k • written 7.7 years ago by
pengchy
▴ 450
0
votes
4
replies
219
views
vector memory exhausted (limit reached?)
escape
seurat
scGSEA
Rstudio.
4 days ago by
50cf32b2
• 0
0
votes
4
replies
1.9k
views
Dating Common Ancestor
ngs
vcf
updated 25 days ago by
Ram
37k • written 8.9 years ago by
Adrian Pelin
★ 2.6k
1
vote
4
replies
1.4k
views
Uniprot to refseq missing entries
uniprot
RNA-Seq
refseq
updated 27 days ago by
Ram
37k • written 7.7 years ago by
jacobsen.jeremy
▴ 40
0
votes
4
replies
3.8k
views
problem in installing zlibbioc library
R
updated 20 days ago by
Ram
37k • written 7.7 years ago by
m_punisher6
• 0
1
vote
4
replies
166
views
trying to look the version of the programs under miniconda3 directory
miniconda3
versions
updated 4 days ago by
ATpoint
68k • written 4 days ago by
v.berriosfarias
▴ 90
0
votes
4
replies
420
views
Error in DNAmAge package in r
methylation
DNAmAge
12 days ago by
andrechristianes
• 0
0
votes
4
replies
442
views
I want to merge gene sequences in fasta to create one genome from all cds region.
file
manipulation
fasta
genome
linux
18 days ago by
iankeetkumar
• 0
0
votes
4
replies
100
views
Getting a VCF file from plink .bed, .fam and .bim files
vcf
plink
3 hours ago by
hi.there
• 0
1
vote
4
replies
421
views
Stringtie issue. "Error: no valid ID found for GFF record"
Stringtie
RNA-seq
updated 18 days ago by
GenoMax
125k • written 19 days ago by
Pegasus
▴ 40
1
vote
4
replies
3.4k
views
BWA MEM alignment output of splited fastq files differ from the original(unsplit) fastq file
next-gen
alignment
updated 24 days ago by
Ram
37k • written 7.7 years ago by
manojkumar_bhosale
▴ 70
4
votes
4
replies
716
views
Analysis of Nanopore cDNA sequencing data
alignment
nanopore
sequencing
minimap2
3 days ago by
Nico80
▴ 60
0
votes
4
replies
248
views
Running command in docker container results in directly shutting down the docker container
docker-container
python
ubuntu
docker
3 days ago by
stan.aanhane
▴ 30
0
votes
4
replies
10k
views
Convert .gbf file to .gbk or .gff
gbk
gff
gbf
updated 11 days ago by
Ram
37k • written 7.7 years ago by
che.bellaj
• 0
3
votes
4
replies
292
views
Renaming fasta headers based on a list
fasta
updated 17 days ago by
Ram
37k • written 18 days ago by
Bertrand
• 0
2
votes
4
replies
336
views
Change sample ID in BAM file to cell barcode
bam
samtools
barcode
scrna
7 days ago by
martin.grasshoff
• 0
2
votes
4
replies
251
views
Ensembl ID to Gene Symbol Converter
ensembl
Homo_sapiens
BioMart
biotools
updated 3 days ago by
GenoMax
125k • written 6 days ago by
GA
• 0
3
votes
4
replies
371
views
Changing Temporary File Location for Local BLASTP to nr Database
temporary
blast
file
protein
nr
12 days ago by
katieostrouchov
▴ 20
0
votes
4
replies
460
views
how to perform gene ontology on genomic data?
GO
18 days ago by
Neel
▴ 10
9
votes
4
replies
5.2k
views
How to analyse normalized read count?
RNA-Seq
R
updated 27 days ago by
Ram
37k • written 7.7 years ago by
pbio
▴ 150
0
votes
3
replies
106
views
Downloading 450k methylation data from GEO
minfi
450K
IDAT
Methylation
GEO
updated 6 hours ago by
GenoMax
125k • written 9 hours ago by
Edward E-B
• 0
2
votes
3
replies
331
views
Creating Gene ID and Gene name colum from FASTA IDs
programming
r
data
FASTA
updated 11 days ago by
barslmn
★ 1.2k • written 11 days ago by
WUSCHEL
▴ 660
3
votes
3
replies
413
views
GO analysis: Different results EnrichGO vs ShinyGO
enrichGO
GO
RNA-seq
shinyGO
analysis
updated 19 days ago by
Jean-Karim Heriche
26k • written 21 days ago by
Clément
▴ 10
0
votes
3
replies
273
views
read 012 matrix
vcftools
updated 21 days ago by
Ram
37k • written 21 days ago by
arwa.ahmad95
• 0
0
votes
3
replies
398
views
What can I do with pan-cancer RNA-seq data that only has FPKM value?
normalization
RNA-seq
updated 26 days ago by
ATpoint
68k • written 26 days ago by
Brisket
▴ 10
0
votes
3
replies
111
views
Help interpreting FastQC report
fastQC
trimming
quality-control
updated 6 hours ago by
GenoMax
125k • written 11 hours ago by
sithlordashley
• 0
0
votes
3
replies
186
views
Reomve the first occurance of overalapping variants from VCF file
vcf
vcftools
updated 6 days ago by
mohammadhassanj
▴ 230 • written 6 days ago by
Frieda
▴ 60
0
votes
3
replies
324
views
How to compare a Nanopore read (.fastq) to a genome assembly file (.fna)
fastq
genome
dna
Nanopore
updated 3 days ago by
colindaven
4.4k • written 13 days ago by
BananaDNA
• 0
1
vote
3
replies
438
views
Using salmon on HISAT2 BAM files for transcript quantification
salmon
alignment
HISAT2
updated 26 days ago by
Buffo
★ 2.0k • written 29 days ago by
skden2020
▴ 10
0
votes
3
replies
208
views
Help converting .CYCHP to .txt or .csv or .vcf
cychp
updated 3 days ago by
Pierre Lindenbaum
152k • written 3 days ago by
Sarah
• 0
0
votes
3
replies
311
views
How to search a .narrowPeak file for specific genes via a batch file
binding
transcription
factor
peaks
updated 26 days ago by
ATpoint
68k • written 26 days ago by
StacyG
• 0
2
votes
3
replies
480
views
Summarizing transcript level annotation from Trinity de novo assembly to gene level annotation
functional
expression
differential
RNAseq
transcriptome
enrichment
Trinity
annotation
genes
13 days ago by
MB
▴ 50
1
vote
3
replies
422
views
Combining TF PWMs
TF
Jaspar
motif
PWM
21 days ago by
rbronste
▴ 410
0
votes
3
replies
325
views
Why genetic PCA method isn't applied in fungi or algae genomic study?
PCA
whole
genome
fungi
sequence
updated 14 days ago by
Jeremy Leipzig
21k • written 15 days ago by
kgwkk2
• 0
0
votes
3
replies
583
views
CDSeq for deconvolution of whole blood RNAseq, any experience?
RNAseq
Deconvolution
updated 5 days ago by
FrankStarling
▴ 20 • written 15 months ago by
Barista
▴ 20
0
votes
3
replies
4.8k
views
Detecting outlier loci from pairwise Fst values
outlier
Fst
vcftools
updated 26 days ago by
Ram
37k • written 7.7 years ago by
Earendil
▴ 50
0
votes
3
replies
271
views
Excluding SNPs from repetitive regions
Population-Genomics
WGS
Variant
VCF
updated 19 days ago by
Pierre Lindenbaum
152k • written 21 days ago by
qstefano
▴ 20
461 results • Page
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You're so close. You can simply loop over sequence dictionaries like you did with the `design_output` and check if the keys with `startswit…
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Have you installed `Xcode` and the command line tools that go with? If not you will need to install those.
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Thanks @genomax I created an aws glue crawler to pull the data from s3://sra-pub-metadata-us-east-1/sra_tax_analysis_tool/ I wonder if it …
Comment: mirbase does not have miRNA annotation of my species, what are the alternatives?
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thanks! however, shouldn't it also have a gtf/gff file with the annotations?
Comment: Getting a VCF file from plink .bed, .fam and .bim files
by
hi.there
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Thanks Ram. Yes. I have read all of this documentation before. --file and --bfile. I have actually tried doing the complete liftover be…
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This data may only be available using `BigQuery` for [**SRA in cloud**][1]. For more information on querying: https://www.ncbi.nlm.nih.g…
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Have a look at ragtag and ragout. I use ragout for smaller assemblies (~20 Mb and less) and ragtag for larger genomes.
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37k
I've been meaning to work on a Biostars-specific code formatting manual for a while now but the basic is pretty simple: You can use backtic…
Comment: Multiline Fasta To Single Line Fasta
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Onur
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Thank you it's also worked for me too. Best,
Comment: CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRl
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Thanks Ram. Could you point to a manual on how to make the post look like yours? I just copy-pasted my R script and this is how it shows in…
Comment: extracting input files form Seurat
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Thank you jared.andrews07
Comment: extracting input files form Seurat
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rasing02
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Yes, I just need the input data so that investigators can use tools other than R to visualize the data in form of viloin plots or feature p…
Comment: Downloading 450k methylation data from GEO
by
GenoMax
125k
I don't think they have provided processed data as a single upload.
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You can get the data behind any of the plots easily enough: ``` p <- VlnPlot(Seurat_object, features = "X", group.by = "Names",split.by…
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