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19
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13
replies
9.9k
views
8 follow
Error installing bcl2fastq 2.20 in make step - Ubuntu 18.04
software error bcl2fastq ubuntu
updated 2.9 years ago by • 0 • written 6.4 years ago by ▴ 140
0
votes
2
replies
858
views
Pseudogenes identification and removal from BRCA samples
NGS
4.5 years ago by smrutimayipanda ▴ 20
0
votes
3
replies
1.1k
views
very low number of reads aligned in bowtie (colourspace)
map colourspace bowtie
updated 4.5 years ago by 154k • written 4.5 years ago by ★ 1.3k
1
vote
1
reply
864
views
Multiple genes comparison
Transcriptome RNA-seq
updated 4.5 years ago by ▴ 160 • written 4.5 years ago by ▴ 10
0
votes
2
replies
1.3k
views
Tools for SNPs and Indels (RNA seq. Nanopore)
Indel RNA-Seq SNP Nanopore
updated 2.7 years ago by 45k • written 4.5 years ago by ▴ 30
4
votes
3
replies
2.0k
views
Complex DESeq2 sample file set up
complex design DESEq2 RNAseq
4.4 years ago by rva_jango ▴ 10
0
votes
0
replies
898
views
Job: Bioinformatician at the Institute of Botany, Czech Academy of Sciences
polyploidization diversification plant
updated 4.4 years ago by 45k • written 4.5 years ago by • 0
0
votes
3
replies
1.4k
views
DESeq2: Variable Importance
DESeq2
updated 4.5 years ago by ★ 90k • written 4.5 years ago by ▴ 30
1
vote
6
replies
2.2k
views
Is BLASTp the quickest method to get a rough idea on ortholog from protein sequence?
blastp ortholog homolog blast
updated 4.5 years ago by 16k • written 4.5 years ago by ▴ 190
0
votes
0
replies
568
views
GOstat error : No results met the specified criteria
RNAseq GO gostat
4.5 years ago by ryme ▴ 30
4
votes
2
replies
1.2k
views
Remote access- data security
Remote-Access
updated 4.5 years ago by ★ 3.4k • written 4.5 years ago by ▴ 110
1
vote
1
reply
1.4k
views
Imputation with Beagle 5.2 for whole exome data at once
Beagle Imputation
updated 4.5 years ago by 2.9k • written 4.5 years ago by ▴ 10
0
votes
2
replies
1.6k
views
Pedigree file for 1k genome , build 38
build 1000G pca 38
4.4 years ago by AVA ▴ 40
5
votes
3
replies
1.6k
views
Why is NNN sequence at the end of chromosomes
Telomere sequence NNN
4.5 years ago by cammm988 ▴ 10
1
vote
1
reply
1.2k
views
How to calculate the *necessary* sequencing depth for a SNP
sequencing SNP analysis depth statistics Sequencing
updated 4.5 years ago by ▴ 730 • written 4.5 years ago by • 0
0
votes
1
reply
870
views
Change genbank files orientation to '5 > '3 based on their ORF direction
reverse genbank ORF complete
updated 4.5 years ago by 22k • written 4.5 years ago by ▴ 10
3
votes
9
replies
2.6k
views
Alternative polyadenylation detection from short-read RNA-seq, software suggestions
software apa alternative-polyadenylation
4.5 years ago by Gregor Rot ▴ 550
2
votes
4
replies
2.4k
views
KRAKEN2 database build ref-seq have some missing data
KRAKEN2 ref-seq
4.4 years ago by jimmy0958073736 ▴ 40
1
vote
4
replies
1.1k
views
How to verify the authenticity of the data set downloaded from database?
data analysis
4.5 years ago by 465336766 • 0
1
vote
6
replies
4.8k
views
bcftools plugin fill-tags with functions
AVG fill-tags bcftools
4.4 years ago by diana.cornejo • 0
3
votes
4
replies
2.0k
views
Duplicate results in vardict vcf
vardict
updated 4.4 years ago by 45k • written 4.5 years ago by ▴ 60
6
votes
4
replies
3.1k
views
Unable to install EnhancedVolcano: non-zero exit status
Harfbuzz EnhancedVolcano R
updated 4.5 years ago by ★ 90k • written 4.5 years ago by ▴ 90
1
vote
2
replies
1.3k
views
How can I format blastn output?
blast pairwise blastn alignment
updated 4.5 years ago by 154k • written 4.5 years ago by • 0
1
vote
4
replies
1.7k
views
PopGenome Not Reading In FASTA File
popgenome MKT selection R phylogenomics
4.5 years ago by Simone ▴ 10
0
votes
1
reply
1.9k
views
error in anvi'o tool
python software error genome R gene
updated 4.5 years ago by • 0 • written 4.7 years ago by ▴ 120
4
votes
1
reply
779
views
Does anyone know if there is an implementation of overlaping kmeans algorithm in R ?
r partitional-clustering kmeans
updated 4.5 years ago by ★ 30k • written 4.5 years ago by ▴ 140
0
votes
2
replies
1.6k
views
How to combine UMIs split across reads 1 and 2 into a single UMI for deduplication?
umitools umi
4.5 years ago by SethG • 0
0
votes
0
replies
925
views
Job: Bioinformatics Job Opening
genomics RNA
updated 4.4 years ago by 45k • written 4.5 years ago by ▴ 110
0
votes
0
replies
566
views
Job: senior bioinformatician, University of Cambridge (UK) - 3years contract
three_years_contract Senior_bioinformatician
4.5 years ago by davide.chiarugi ▴ 20
4
votes
5
replies
15k
views
Extract rows name in R
rows R
updated 4.5 years ago by 12k • written 4.5 years ago by ▴ 30
0
votes
1
reply
1.2k
views
How two merge two different interactome networks?
Network analysis Network merge
updated 4.5 years ago by ▴ 70 • written 4.7 years ago by • 0
1
vote
2
replies
1.3k
views
Download MuSiC RNAseq analysis program
devtools MuSiC RNAseq
4.5 years ago by - • 0
0
votes
0
replies
686
views
Job: Postdoctoral Associate - 121648
DHVI Duke Postdoc
updated 4.4 years ago by 45k • written 4.5 years ago by • 0
0
votes
0
replies
1.0k
views
Artic protocol
variant-calling artic nanopre sars-cov-2 medaka
4.5 years ago by juanjo75es ▴ 130
2
votes
3
replies
2.2k
views
How to change my SNP Id format from chr1_847228_C_T to chr1_847228 in my .bim file.
Chromosome SNP position Plink unix rsid
updated 4.5 years ago by ★ 4.8k • written 4.5 years ago by ▴ 20
1
vote
3
replies
2.1k
views
PGS Catalog file does not have rsID
Catalog CAD PGS PRSice
updated 4.2 years ago by ★ 4.8k • written 4.5 years ago by ▴ 20
0
votes
0
replies
538
views
I see SNP in IGB but not in my .vcf file
mapping snp
updated 4.5 years ago by 45k • written 4.5 years ago by • 0
5
votes
2
replies
1.7k
views
Kallisto alignment method for single nuclei
Kallisto
updated 4.5 years ago by ★ 7.8k • written 4.5 years ago by ▴ 20
3
votes
8
replies
7.2k
views
Plink update name flag, setting column names
plink update-name
updated 4.5 years ago by 12k • written 4.6 years ago by ▴ 70
1
vote
1
reply
2.0k
views
How to trim adaptor sequences for NEBNext kit
fastq trimmomatic RNA-seq
updated 4.5 years ago by 154k • written 4.5 years ago by ▴ 10
0
votes
0
replies
951
views
Confused about sambamba syntax for unmapped and mapped
sambamba
4.5 years ago by DNAngel ▴ 260
1
vote
0
replies
569
views
Finding Variants Unique to a Subset of Samples in a Multi-Sample VCF File
Data VCF Filtering
updated 4.4 years ago by 45k • written 4.5 years ago by ▴ 10
6
votes
10
replies
3.8k
views
Gaps in alignment
NGS mem bwa alignment
4.5 years ago by mikegrootde ▴ 20
3
votes
5
replies
1.7k
views
Identifying introns
RNA-Seq
updated 4.4 years ago by 45k • written 4.5 years ago by ▴ 70
0
votes
0
replies
474
views
Binding site mutation
RDRP NSP12
4.5 years ago by Mohamed Elsherbieny • 0
0
votes
1
reply
1.4k
views
GDC Client 500 Server Error
TCGA GDC error GDC-client server
updated 4.5 years ago by ★ 90k • written 4.5 years ago by ▴ 10
0
votes
4
replies
2.0k
views
Make doesn't work for Allpaths LG
allpaths error make lg
4.5 years ago by cybercat • 0
6
votes
6
replies
8.9k
views
6 follow
ClusterProfiler-cnetplot output to Cytoscape?
pathway clusterprofiler
updated 4.3 years ago by • 0 • written 9.1 years ago by ▴ 10
0
votes
0
replies
810
views
Different no of 'unknown/class u' transcripts in merged.gtf and final.gtf files
Cufflinks StringTie GffCompare RNA-Seq
4.5 years ago by SKY ▴ 60
0
votes
1
reply
9.4k
views
Difference between "Original tree" and "Bootstrap consensus tree" in Mega X software for phylogeny
Mega Phylogeny
updated 4.5 years ago by • 0 • written 5.0 years ago by ★ 1.4k
122,198 results • Page 641 of 2444
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Answer: Midpoint rooting IQTREE newick file moves node support around
Answer: Subsetting before QC in Spatial Transcriptomics
Answer: Feature Counts vs Salmon quantification
Comment: Feature Counts vs Salmon quantification
Answer: Can i use orthofinder for small protein datasets and not full proteome?
Comment: Comparison of different RNAseq data sets
Comment: ID unifiying across different datasets
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Comment: Subsetting before QC in Spatial Transcriptomics by Kent ▴ 30
Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
Comment: Midpoint rooting IQTREE newick file moves node support around by Luca Arbore ▴ 10
Thank you very much Kevin, it worked!
Comment: ID unifiying across different datasets by GenoMax 154k
In this case the entry notes that this is likely the product of a pseudogene: https://www.uniprot.org/uniprotkb/Q5VTE0/entry and existence …
Comment: Comparison of different RNAseq data sets by DrSmad ▴ 10
Each lab contributes both control and LPS. Example, for cell line A_lab1 did and analysis on control and LPS-6h. Cell line B_lab2 did contr…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
sorry, why some gene names are often lacking though the Uniprot ID is still valid (using biomart)?
Comment: snpEff: Unsupported structural variant types by shpak.max ▴ 70
Unfortunately, while it ran without a problem initially, when I checked the run screen today, I saw the following error message (and unlike…
Comment: ID unifiying across different datasets by GenoMax 154k
You can use the [**ID mapping tool**][1] from UniProt site (third ID did not map from the list above): From To P68104 ENSG0000015…
Answer: The geo samples is not having sentrix id and sentrix position. But this informat by yura.grabovska ▴ 890
Crosspost from related question: https://www.biostars.org/p/9616466/#9616534 ``` ##Using R, illuminaio from Bioconductor library(…
Answer: Finding Sentrix ID in HM450K arrays by yura.grabovska ▴ 890
``` ##Using R, illuminaio from Bioconductor library(illuminaio) temp.idat <- readIDAT(file = "200379120087_R02C02_Grn.idat") tem…
Comment: Can i use orthofinder for small protein datasets and not full proteome? by michael.ante ★ 4.0k
Do you want to compare them by sequence or by function? For the later, you can use e.g. InterProScan, KoFamScan.
Answer: Can i use orthofinder for small protein datasets and not full proteome? by dthorbur ★ 3.2k
If you're just using the tool for clustering purposes, I think OrthoFinder might be a little clunky and would recommend using something lik…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
Thank you; The problem is let's say in the protein ID column I see `Q5VTE0;P68104;Q05639` here I am sure I should get which `ENSG` for eac…
Comment: How to improving 2-Nucleotide RNA-seq Mapping Accuracy by 2411110159 • 0
Since we do not have real data yet, I tried to simulate this using strand-specific RNA bisulfite-seq reads (C to T). Read1 corresponds to t…
Comment: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies by 2411110159 • 0
Very helpful!
Comment: direct RNA long-reads alignment against reference genome by frarodmar17 • 0
Okay, thanks! I removed reads.fa and I used the index created with minimap2 in .mmi format. Is this correct?
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