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152
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Aspera: Failed to authenticate
ENA aspera
updated 36 minutes ago by • 0 • written 5 days ago by ▴ 40
0
votes
0
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13
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How long does it take to carry out the GWAS workflow?
plink IMPUTE2 SHAPEIT2 GWAS GCTA
58 minutes ago by s2060266 • 0
0
votes
0
replies
11
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If four groups (2 cell lines +/- treatments) of single cell RNA seq available, do I have to analyze each of the four datasets seperately?
scRNA-seq Seurat cellranger
1 hour ago by mrj ▴ 60
0
votes
1
reply
99
views
Does the SOAP (BGI) website mirror exist
software SOAP
updated 1 hour ago by • 0 • written 26 days ago by ▴ 210
0
votes
1
reply
66
views
ggplot split jitter within grouped boxes by different variables
jitter Rstudio R ggplot
updated 2 hours ago by ▴ 520 • written 7 hours ago by • 0
3
votes
3
replies
153
views
Importance of Multiple Sequence Alignment
Multiple Acceleration Sequence MAFFT Alignment Hardware
updated 2 hours ago by ★ 14k • written 23 hours ago by • 0
0
votes
0
replies
27
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Processing paired end miRNA reads for use with mirdeep2?
rna-seq mirna merging mirdeep2 mirna-seq
4 hours ago by AT • 0
1
vote
2
replies
75
views
hisat2 /usr/bin/env: ‘python’: No such file or directory
process erroe hisat2
updated 4 hours ago by ★ 14k • written 6 hours ago by • 0
0
votes
1
reply
65
views
Loop for merging multiple BAM files from multiple lanes with different names into related names/ samstat
samtools chipseq samstat
updated 5 hours ago by 107k • written 8 hours ago by • 0
622
votes
157
replies
72k
views
93 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
handbook tutorial training News
updated 2 days ago by 270 • written 4.9 years ago by 90k
0
votes
0
replies
28
views
Error with Treemix input file
Treemix Ubuntu
4 hours ago by Camila Martínez • 0
0
votes
0
replies
41
views
Job: Postdoctoral Fellow: Biological Sciences, JG-Joint Genome Institute
Postdoctoral Sciences Biological Fellow
updated 1 hour ago by 90k • written 6 hours ago by ▴ 50
0
votes
1
reply
73
views
Problem in plotting graph or Graphics Device in the RStudio
R NullDevice plot
updated 6 hours ago by ★ 1.5k • written 11 hours ago by • 0
0
votes
1
reply
62
views
How to do gene enrichment with locally stored KEGG & Reactome data in R
R enrichment
updated 7 hours ago by ★ 1.5k • written 7 hours ago by • 0
8
votes
22
replies
4.1k
views
9 follow
bcl2fastq with xGen Dual Index UMI Adapters to produce 3 read and 2 index fastqs
rna-seq
updated 9 hours ago by • 0 • written 2.1 years ago by ▴ 20
0
votes
3
replies
104
views
Exome sequencing one sample on two lanes considered two read groups for marking of PCR duplicates?
deduplication read groups exome sequencing
updated 9 hours ago by 107k • written 9 hours ago by • 0
2
votes
2
replies
163
views
VCF to fasta incorporating heterozygous sites
fasta heterozygous VCF unphased
10 hours ago by Sarah ▴ 20
3
votes
4
replies
787
views
VEP allele frequency from gnomAD genomes
vep allele frequency gnomad genomes
updated 10 hours ago by • 0 • written 8 months ago by • 0
2
votes
2
replies
103
views
Convert transcriptomic bam to genomic bam
genome bisulfite bam transcriptome
6 hours ago by joe ▴ 230
0
votes
0
replies
161
views
Job: Postdoctoral Researcher, Maastricht University | 'Bioinformatics/Cheminformatics (4 yrs), using OpenAPI, FAIR, and Docker for predictive toxicology a…
OpenAPI FAIR Bioinformatics Docker Cheminformatics
11 hours ago by secretariat-bigcat • 0
0
votes
0
replies
61
views
Job: PhD Candidate Maastricht University | 'Using Ontologies to build a Knowledge Graph for Molecular Interactions of Nanoparticles'
Bioinformatics PhD Interactions Nanoparticles Molecular
11 hours ago by secretariat-bigcat • 0
0
votes
0
replies
34
views
Annotation of differentially methylated region or based in methylkit using genomation, how to find annotation file?
methylkit epeigenetics R methylation differential analysis DNA
12 hours ago by harshraje19 ▴ 40
4
votes
5
replies
137
views
6 follow
the way to find pseudogenes in my scaffolds of genome
pseudogene
written 15 hours ago by ▴ 10
1
vote
2
replies
97
views
how to map Pacbio CCS fastq
minimap2 Pacbio
updated 12 hours ago by ▴ 20 • written 20 hours ago by • 0
0
votes
0
replies
28
views
Labelling SNPs in a stacked manhattan plot with karyoploteR
manhattan gwas plot karyoploteR
12 hours ago by jsreddy • 0
0
votes
1
reply
72
views
What does it "mean" when MrBayes chooses rtREV as substitution model?
mrbayes substitution phylogeny matrix
updated 12 hours ago by ★ 14k • written 15 hours ago by 49k
0
votes
0
replies
39
views
Anyone could help me with cutadapt?
Cutadapt trim primer
updated 11 hours ago by 107k • written 12 hours ago by • 0
0
votes
0
replies
33
views
cpan install Bio::PrimerDesigner
CPAN Bioinformatics
12 hours ago by shahbazmunir11 ▴ 10
1
vote
1
reply
73
views
alternative splicing: very different outputs from rMATS vs altanalyze
alternative rMATS splicing altanalyze
updated 12 hours ago by 13k • written 13 hours ago by ▴ 10
2
votes
2
replies
147
views
Is it possible to integrate shell scripts in snakemake
Bioinformatics
updated 13 hours ago by ▴ 50 • written 3 days ago by • 0
3
votes
1
reply
100
views
Colour UMAP based on expression of multiple genes
visualisation scRNAseq ggplot
13 hours ago by Ciaran ▴ 20
0
votes
0
replies
30
views
no restriction enzyme in process_radtags
process_radtags restriction stacks enzyme
13 hours ago by strive • 0
0
votes
0
replies
32
views
Mouse RefCDS for dNdScv package
musculus dndscv mus refcds mouse
14 hours ago by isd1989 • 0
0
votes
2
replies
117
views
GTF upload error UCSC related to stradedness
genome browser RNAseq gtf UCSC
updated 14 hours ago by ★ 1.4k • written 1 day ago by • 0
1
vote
1
reply
90
views
Methylation coordinates for hg19
methylation cpg
updated 14 hours ago by ▴ 50 • written 1 day ago by ★ 1.6k
2
votes
3
replies
133
views
Counting the number of SNPs (VCF) for each genomic coordinates (BED)
vcf vcftools bed bedtools
updated 14 hours ago by ▴ 80 • written 16 hours ago by ▴ 50
0
votes
8
replies
315
views
Recommended mapper
alignment metagenomics Mapping
9 hours ago by biobiu ▴ 120
0
votes
1
reply
86
views
how to interpret very short effective length in Salmon output
RNASEQ salmon
updated 14 hours ago by 90k • written 2 days ago by • 0
0
votes
2
replies
79
views
EBI European Nucleotide Archive (ERA) aspera access broken
elixir ebi ena
updated 14 hours ago by 13k • written 14 hours ago by ★ 2.6k
0
votes
1
reply
94
views
Diamond and Taxonomic information
daa megan taxonomy Diamond
updated 14 hours ago by 90k • written 1 day ago by ▴ 30
6
votes
7
replies
289
views
How to understand logics and statistical concepts behind limma package?
R microarray DGE limma
updated 14 hours ago by 107k • written 2 days ago by ▴ 40
2
votes
2
replies
101
views
Sort a sub column within a column while keeping the feature (LINUX)
na
updated 15 hours ago by ▴ 80 • written 15 hours ago by • 0
1
vote
1
reply
101
views
Extracting named fasta sequences according to list with Biopython
Biopython FASTA
updated 15 hours ago by 90k • written 1 day ago by • 0
2
votes
3
replies
175
views
I'm not sure my Bulk RNAseq read counts extracted from fastq file are correct
fastq RNAseq raw-count
updated 11 hours ago by 11k • written 21 hours ago by • 0
0
votes
1
reply
109
views
About Foreign Fields in VCF (4.3)
call tab format vcf delimited variant
updated 9 hours ago by 46k • written 16 hours ago by ★ 1.1k
0
votes
0
replies
33
views
Fetch rsid and related genotype/sample from vcf file
rsid vcf file and
16 hours ago by Nai • 0
0
votes
0
replies
35
views
For DE analysis, should I exclude all the samples that don't have the data of normal tissue?
TCGA RNA-seq DE
17 hours ago by Sonia • 0
0
votes
1
reply
58
views
KOBAS on Galaxy local
Galaxy KOBAS
updated 17 hours ago by 12k • written 18 hours ago by • 0
0
votes
0
replies
32
views
How to include a Jmol Console Script in a Python Script
Python Jmol Script
18 hours ago by kbaitsi • 0
3
votes
2
replies
278
views
In single cell RNA-seq, do we perform regular quality checks and adapter trimming before using cellranger?
cellranger adapter_trimming QC scRNA-seq
6 hours ago by mrj ▴ 60
95,961 results • Page 1 of 1920
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Answer: Extracting named fasta sequences according to list with Biopython
How do I compare the relative levels of gene expression and DNA methylation for 33 cancers retrieved from TCGA Pancan dataset?
Answer: Importance of Multiple Sequence Alignment
Comment: Importance of Multiple Sequence Alignment
Answer: Importance of Multiple Sequence Alignment
NCBI NR protein db nr.gz FASTA inflate error?
Answer: NCBI NR protein db nr.gz FASTA inflate error?
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Answer: Aspera: Failed to authenticate by mckalem • 0
I also have the same problem. Did you figure it out?
Answer: Does the SOAP (BGI) website mirror exist by 410380015 • 0
[soap2.21release.tar.gz][1] [1]: https://pan.baidu.com/s/1tKPbKd5yjb1xCVdI4b_N-w
Comment: IDR installation help by Jianyu ▴ 520
I think "--prefix" is to specify the directory where lib locates? So it should be "/User/myhomedir/Library/Python/3.8/"
Answer: ggplot split jitter within grouped boxes by different variables by Jianyu ▴ 520
I didn't rebuild your dataset, could you try the code below? I think it should work ggplot(ELISAtot) + geom_boxplot(aes(x = …
Answer: Importance of Multiple Sequence Alignment by Mensur Dlakic ★ 14k
> I found in publications that some of the MAFFT algorithms are more accurate compared to other solutions for MSA but their adoption in Ind…
Answer: hisat2 /usr/bin/env: ‘python’: No such file or directory by Mensur Dlakic ★ 14k
This error means one of the two things: 1) you don't have a system-wide installation of python; 2) your have python installed but it is not…
Comment: Searching metagenomic datasets for a specific species by Sarah • 0
Thank you for your help!
Comment: Empty output from UMItools dedup after fastp processing by i.sudbery 13k
That is very werid. The file should at least be created, even if nothing goes into it. Can you run the same command without either the `-S`…
Answer: Loop for merging multiple BAM files from multiple lanes with different names int by GenoMax 107k
Here is one way to do this: We are starting with these files $ ls -1 *.bam HCT116_Input_S50_L001_R1_001.bam HCT116_Input_S50_…
Comment: hisat2 /usr/bin/env: ‘python’: No such file or directory by GenoMax 107k
How did you install `hisat2`? Using `conda`?
Comment: Convert transcriptomic bam to genomic bam by joe ▴ 230
Wow, thank you...you have saved me oh so much time. Biostars for the win :)
Comment: In single cell RNA-seq, do we perform regular quality checks and adapter trimmin by mrj ▴ 60
Thank you for the answer
Answer: Problem in plotting graph or Graphics Device in the RStudio by Papyrus ★ 1.5k
The function is generating and saving the plot as a PDF file in your working directory, instead of showing it to you. If you want the plot …
Comment: Empty output from UMItools dedup after fastp processing by c.heininger • 0
I don't even get a log file as an output, which just adds to my confusion
Comment: How to do gene enrichment with locally stored KEGG & Reactome data in R by Papyrus ★ 1.5k
For example, the [goseq][1] package can be used with any custom file describing pathways/gene sets to perform enrichment analysis. (There i…
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