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121,319 results • Page 622 of 2427
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3
votes
4
replies
1.7k
views
Duplicate ID error with update-name flag
Chromosome SNP position Plink unix rsid
updated 4.0 years ago by 12k • written 4.0 years ago by ▴ 20
0
votes
1
reply
1.1k
views
Generating multiple species consensus alignments for tree topology tests
bcftools alignment fasta iqtree vcf
updated 4.0 years ago by ▴ 160 • written 4.0 years ago by ▴ 40
1
vote
8
replies
1.8k
views
How to map rsIDs to KEGG variant Ids
dbsnp kegg rsid
4.0 years ago by david.f.stein ▴ 10
0
votes
1
reply
950
views
blastn cut off values
blast
updated 4.0 years ago by ▴ 160 • written 4.0 years ago by ▴ 50
2
votes
1
reply
5.3k
views
vcftools and SnpSift give different values for Ts/Tv ratio
variant SNP vcf transversion transition
updated 3.6 years ago by 45k • written 10.3 years ago by ▴ 380
12
votes
6
replies
10k
views
6 follow
convert sam into paf format
genome alignment sequencing assembly SNP
updated 2.4 years ago by ▴ 30 • written 4.5 years ago by ▴ 10
0
votes
4
replies
1.2k
views
add text to a path by adding text to it with python (FTP Path NCBI)
python ncbi pandas
4.0 years ago by Debut ▴ 20
1
vote
0
replies
864
views
Job: Opportunity: Bioinformatics Software Engineer - Bioinformatics Core @ Memorial Sloan Kettering Cancer Center, New York, NY (US)
cancer_biology Python R
updated 4.0 years ago by 45k • written 4.0 years ago by ▴ 10
0
votes
1
reply
731
views
Differential Expression Analysis Using RPKM
RPKM RNA-seq DE
updated 4.0 years ago by 15k • written 4.0 years ago by • 0
1
vote
1
reply
939
views
Single cell clusters annotating to same cell-type
Monocle Single-cell Seurat Pseudotime
updated 4.0 years ago by ★ 1.1k • written 4.0 years ago by ▴ 30
0
votes
2
replies
1.1k
views
Exact duplicated reads between independent replicates
ChIP NGS low-input duplicates Illumina
4.0 years ago by Miguel • 0
0
votes
1
reply
1.7k
views
Surat object UMAP - highlight cells based on Citeseq data
Seurat UMAP
updated 4.0 years ago by 3.2k • written 4.0 years ago by ▴ 40
2
votes
1
reply
957
views
Obtaining all independent SNPs
SNPs permutation pruning clumping PLINK
updated 4.0 years ago by ★ 4.8k • written 4.0 years ago by ▴ 10
1
vote
2
replies
1.1k
views
Cytoscape for co-occurence network analysis
Microbiome 16S analysis Cytoscape Network
4.0 years ago by Bioinfonext ▴ 470
3
votes
2
replies
2.1k
views
Structural variants calling in a population
structural variants
updated 4.0 years ago by • 0 • written 8.0 years ago by ★ 1.0k
5
votes
4
replies
6.7k
views
Merge vcf files of structural variants
structural_variants vcf merge
updated 4.0 years ago by • 0 • written 6.8 years ago by ▴ 20
3
votes
2
replies
3.8k
views
For loop to parallel run commands
Unix bash Linux
4.0 years ago by endretoth ▴ 40
19
votes
13
replies
9.4k
views
8 follow
Error installing bcl2fastq 2.20 in make step - Ubuntu 18.04
software error bcl2fastq ubuntu
updated 2.5 years ago by • 0 • written 5.9 years ago by ▴ 140
0
votes
2
replies
735
views
Pseudogenes identification and removal from BRCA samples
NGS
4.0 years ago by smrutimayipanda ▴ 20
0
votes
3
replies
925
views
very low number of reads aligned in bowtie (colourspace)
map colourspace bowtie
updated 4.0 years ago by 151k • written 4.0 years ago by ★ 1.3k
1
vote
1
reply
719
views
Multiple genes comparison
Transcriptome RNA-seq
updated 4.0 years ago by ▴ 160 • written 4.0 years ago by ▴ 10
0
votes
2
replies
1.1k
views
Tools for SNPs and Indels (RNA seq. Nanopore)
Indel RNA-Seq SNP Nanopore
updated 2.2 years ago by 45k • written 4.0 years ago by ▴ 30
4
votes
3
replies
1.6k
views
Complex DESeq2 sample file set up
complex design DESEq2 RNAseq
3.9 years ago by rva_jango ▴ 10
0
votes
0
replies
784
views
Job: Bioinformatician at the Institute of Botany, Czech Academy of Sciences
polyploidization diversification plant
updated 4.0 years ago by 45k • written 4.0 years ago by • 0
0
votes
3
replies
1.2k
views
DESeq2: Variable Importance
DESeq2
updated 4.0 years ago by 89k • written 4.0 years ago by ▴ 30
1
vote
6
replies
1.8k
views
Is BLASTp the quickest method to get a rough idea on ortholog from protein sequence?
blastp ortholog homolog blast
updated 4.0 years ago by 15k • written 4.0 years ago by ▴ 190
0
votes
0
replies
496
views
GOstat error : No results met the specified criteria
RNAseq GO gostat
4.0 years ago by ryme ▴ 30
4
votes
2
replies
951
views
Remote access- data security
Remote-Access
updated 4.0 years ago by ★ 3.4k • written 4.0 years ago by ▴ 100
1
vote
1
reply
1.2k
views
Imputation with Beagle 5.2 for whole exome data at once
Beagle Imputation
updated 4.0 years ago by 2.9k • written 4.0 years ago by ▴ 10
0
votes
2
replies
1.3k
views
Pedigree file for 1k genome , build 38
build 1000G pca 38
4.0 years ago by AVA ▴ 40
5
votes
3
replies
1.3k
views
Why is NNN sequence at the end of chromosomes
Telomere sequence NNN
4.0 years ago by cammm988 ▴ 10
1
vote
1
reply
964
views
How to calculate the *necessary* sequencing depth for a SNP
sequencing SNP analysis depth statistics Sequencing
updated 4.0 years ago by ▴ 720 • written 4.0 years ago by • 0
0
votes
1
reply
709
views
Change genbank files orientation to '5 > '3 based on their ORF direction
reverse genbank ORF complete
updated 4.0 years ago by 22k • written 4.0 years ago by ▴ 10
3
votes
9
replies
2.1k
views
Alternative polyadenylation detection from short-read RNA-seq, software suggestions
software apa alternative-polyadenylation
4.0 years ago by Gregor Rot ▴ 550
2
votes
4
replies
2.1k
views
KRAKEN2 database build ref-seq have some missing data
KRAKEN2 ref-seq
3.9 years ago by jimmy0958073736 ▴ 40
1
vote
4
replies
977
views
How to verify the authenticity of the data set downloaded from database?
data analysis
4.0 years ago by 465336766 • 0
1
vote
6
replies
3.5k
views
bcftools plugin fill-tags with functions
AVG fill-tags bcftools
4.0 years ago by diana.cornejo • 0
3
votes
4
replies
1.7k
views
Duplicate results in vardict vcf
vardict
updated 4.0 years ago by 45k • written 4.0 years ago by ▴ 60
6
votes
4
replies
2.6k
views
Unable to install EnhancedVolcano: non-zero exit status
Harfbuzz EnhancedVolcano R
updated 4.0 years ago by 89k • written 4.0 years ago by ▴ 90
1
vote
2
replies
1.1k
views
How can I format blastn output?
blast pairwise blastn alignment
updated 4.0 years ago by 151k • written 4.0 years ago by • 0
1
vote
4
replies
1.4k
views
PopGenome Not Reading In FASTA File
popgenome MKT selection R phylogenomics
4.0 years ago by Simone ▴ 10
0
votes
1
reply
1.6k
views
error in anvi'o tool
python software error genome R gene
updated 4.0 years ago by • 0 • written 4.3 years ago by ▴ 120
4
votes
1
reply
680
views
Does anyone know if there is an implementation of overlaping kmeans algorithm in R ?
r partitional-clustering kmeans
updated 4.0 years ago by ★ 29k • written 4.0 years ago by ▴ 140
0
votes
2
replies
1.3k
views
How to combine UMIs split across reads 1 and 2 into a single UMI for deduplication?
umitools umi
4.0 years ago by SethG • 0
0
votes
0
replies
847
views
Job: Bioinformatics Job Opening
genomics RNA
updated 4.0 years ago by 45k • written 4.0 years ago by ▴ 80
0
votes
0
replies
488
views
Job: senior bioinformatician, University of Cambridge (UK) - 3years contract
three_years_contract Senior_bioinformatician
4.0 years ago by davide.chiarugi ▴ 20
4
votes
5
replies
14k
views
Extract rows name in R
rows R
updated 4.0 years ago by 12k • written 4.0 years ago by ▴ 30
0
votes
1
reply
982
views
How two merge two different interactome networks?
Network analysis Network merge
updated 4.0 years ago by ▴ 70 • written 4.2 years ago by • 0
1
vote
2
replies
1.0k
views
Download MuSiC RNAseq analysis program
devtools MuSiC RNAseq
4.0 years ago by - • 0
0
votes
0
replies
594
views
Job: Postdoctoral Associate - 121648
DHVI Duke Postdoc
updated 4.0 years ago by 45k • written 4.0 years ago by • 0
121,319 results • Page 622 of 2427
Recent Votes
WGCNA modules and categorical traits relationship
Comment: nanopore unaligned bam files
Answer: Discussions about QC of sc-multiomic-ATAC_RNA-seq from 10xgenomics platform in t
Answer: Discussions about QC of sc-multiomic-ATAC_RNA-seq from 10xgenomics platform in t
Answer: WGCNA blockwiseModules function for small datasets
Answer: WGCNA blockwiseModules function for small datasets
A: bcftools selest sites with FILTER "PASS" or "."
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Recent Replies
Comment: normalize between 2 different platform by 1364454115 • 0
Hello, Could you please tell me whether different datesets generated by multiplex PCR and 5'UMI-tagged 5′-RACE can be analyzed together? T…
Comment: Discussions about QC of sc-multiomic-ATAC_RNA-seq from 10xgenomics platform in t by gynecoloji • 0
Thanks for your response. I think it may be better to keep those repetitive regions and only filter out the blacklisted regions. This is a …
Comment: Discussions about QC of sc-multiomic-ATAC_RNA-seq from 10xgenomics platform in t by jared.andrews07 ★ 18k
IDR addresses a different problem than removal of reads aligning to blacklist reads, though it's unquestionably useful for deriving more ro…
Comment: Issue with Package installation in R. by GenoMax 151k
Simply posting a snippet of error message in a question is the reason you have not received any responses. Please make an effort to formu…
Answer: Building database with snpEff -- -gtf22 option not recognized/file not read by michael.dhar • 0
Based on the ordering of the commands here: https://github.com/pcingola/SnpEff/issues/583 I believe I just needed to place the "build" c…
Comment: WGCNA blockwiseModules function for small datasets by ATS ▴ 10
That's great to know. Thanks for your input!
Answer: Discussions about QC of sc-multiomic-ATAC_RNA-seq from 10xgenomics platform in t by LChart 5.0k
It should be noted that concerns about mapping artifacts in ChIP-seq really come from an era where reads were 36bp (or even 25bp!) in lengt…
Comment: WGCNA pickSoftThreshold problem by LChart 5.0k
AGain you seem to be over-filtering. Your mean.k and median.k are really low, so I think the number of input genes you used for this is ver…
Answer: Discussions about QC of sc-multiomic-ATAC_RNA-seq from 10xgenomics platform in t by jared.andrews07 ★ 18k
I am going to guess you've seen/thoroughly read [this paper about the ENCODE blacklist regions](https://www.nature.com/articles/s41598-019-…
Comment: Using VEP custom input by Sd • 0
Initially, I converted the file to GFF3 format in order to run VEP, but I got warnings and couldn’t figure out what the problem was. GFF…
Comment: nanopore unaligned bam files by colindaven 7.6k
When you have a bam make sure you check the methyl tags MM and ML are present. Something like samtools view -h x.bam | grep MM sam…
Comment: nanopore unaligned bam files by sarahmanderni ▴ 130
yes keeping both mapping info and methylation info at the same time is the intention. Thanks so much for the reosponse! I will try it
Comment: nanopore unaligned bam files by GenoMax 151k
> OP wants to align AND keep the methylation info Then use something like minimap2 -t use_N_cores -Y -y -ax map-ont your_minimap_ind…
Comment: nanopore unaligned bam files by lieven.sterck 15k
I think OP wants to align AND keep the methylation info, which is indeed the tricky part ... Not entirely sure but I think the `dorado ali…
Answer: nanopore unaligned bam files by GenoMax 151k
> is this normal to receive the bam files in this shape and Yes. If you asked for methylation calls then this is a way to capture that i…
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