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121,912 results • Page 699 of 2439
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1
vote
5
replies
1.2k
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Low mapping percent (whole metagenome shotgun assembly)
whole metagenome shotgun sequencing illumina
4.5 years ago by mewgia • 0
2
votes
2
replies
1.8k
views
problem with download fastq file from SRA
RNA-Seq
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 40
2
votes
1
reply
833
views
TEdenovo blasting with Recon perpetuates..!
TEdenovo REPET TE
4.5 years ago by mthm ▴ 80
2
votes
3
replies
1.1k
views
Minimum overlap when comparing BED files
bedtools
4.5 years ago by pablo.anton.garcia • 0
0
votes
0
replies
825
views
circlize output image problem
circlize chord diagram
4.5 years ago by aminijavad4 ▴ 10
0
votes
1
reply
1.2k
views
WGCN visualize one module
RNA-Seq WGCNA Igraph Network
updated 4.4 years ago by • 0 • written 4.5 years ago by • 0
2
votes
1
reply
748
views
How to validate artificially generated enhancers ?
sequencing ChIP-Seq genome machine Learning
4.5 years ago by ahteshamabbasi1996 ▴ 10
1
vote
2
replies
1.3k
views
The parameter of HISAT2 and samtools
RNA-Seq
updated 4.5 years ago by ▴ 480 • written 4.5 years ago by • 0
0
votes
3
replies
1.0k
views
Must an experimentally proven disease-relevant gene appear significantly differentially expressed on RNA sequencing analysis?
RNA-Seq rna-seq R next-gen
4.5 years ago by charlesgwellem ▴ 10
1
vote
0
replies
552
views
Integrative analysis of RNA-Seq and Chip-Seq data in R
RNA-Seq ChIP-Seq R
4.5 years ago by g.koorsen ▴ 10
6
votes
2
replies
1.0k
views
Find out common genes in our dataset
RNA-seq
updated 2.1 years ago by 45k • written 4.5 years ago by • 0
0
votes
0
replies
829
views
R-Nb Clust. Can you acces alternative -not best- clustering partitions?
R cluster NbClust
updated 4.5 years ago by 89k • written 4.5 years ago by • 0
0
votes
0
replies
1.0k
views
News: Spring Bioinformatics Courses @ Edinburgh Genomics
metagenomics RNA-Seq SNP training
updated 2.6 years ago by 45k • written 4.5 years ago by ▴ 40
7
votes
7
replies
2.4k
views
How to extract postions from gnomad using tabix?
tabix gnomad vcf
updated 4.5 years ago by 166k • written 4.5 years ago by ★ 4.4k
0
votes
0
replies
440
views
scRNA-seq cell type annotation
RNA-Seq
4.5 years ago by chituchibubao • 0
0
votes
0
replies
812
views
DrugBank data extraction using dbparser
drug Drugbank drug-gene R dbparser
4.5 years ago by srijanibagchi • 0
0
votes
3
replies
2.8k
views
Can you generate ASVs from pre-merged paired-end reads?
ASV OTU dada2 qiime2 16S
updated 4.5 years ago by ▴ 30 • written 4.5 years ago by • 0
1
vote
2
replies
793
views
Getting reference sequence for set of reads
RNA-Seq alignment samtools bedtools
updated 4.5 years ago by 20 • written 4.6 years ago by • 0
0
votes
1
reply
907
views
Create a regulatory network between exosomal and endogenous miRNAs
miRNA Exosomal endogenous piRNA smallRNA-seq
updated 4.5 years ago by ▴ 270 • written 4.5 years ago by ▴ 80
0
votes
0
replies
843
views
Chimeric reads with STAR
RNA-Seq genome alignment
4.5 years ago by FarnazTabrizi95 • 0
0
votes
0
replies
881
views
How many GBS derived reads pass filters after demultiplexing, adapter removal, trimming and filtering?
GBS SNP Stacks Cutadapt
4.5 years ago by giulia.trauzzi ▴ 30
4
votes
12
replies
3.1k
views
Remove Chr:position format to just Chr
imputation PRSice CHR
updated 4.5 years ago by ★ 4.8k • written 4.5 years ago by • 0
0
votes
0
replies
656
views
PSI(Percent spliced-in) Difference test
RNA-Seq
4.5 years ago by fuhaolll2 ▴ 30
1
vote
2
replies
3.1k
views
Filter field are all ".", no "PASS" in vcf file ?
software error next-gen sequencing genome
updated 4.5 years ago by • 0 • written 11.0 years ago by ▴ 110
0
votes
0
replies
2.3k
views
PGLS in R - nlme:gls VS caper:pgls - non-ultrametric tree & negative lambda values
r pgls negative-lambda non-ultrametric tree
4.5 years ago by gabry.scata • 0
0
votes
3
replies
1.7k
views
to annotate BEDPE files
bedtools annotate
updated 24 months ago by ▴ 760 • written 4.5 years ago by ★ 1.4k
0
votes
4
replies
1.8k
views
RepeatModeler:Input has potential formatting error
assembly
updated 4.5 years ago by ▴ 940 • written 4.5 years ago by ▴ 20
0
votes
1
reply
1.3k
views
News: Results are now Available for the precisionFDA Truth Challenge V2
genome
updated 2.6 years ago by 45k • written 5.1 years ago by ▴ 150
0
votes
3
replies
1.8k
views
Removing batch effects
batch-effect RNA-Seq
updated 4.5 years ago by 15k • written 4.5 years ago by ▴ 30
4
votes
7
replies
3.2k
views
How to extract sequences from multiple fastq files based on part of the header?
sequencing
updated 4.5 years ago by 13k • written 4.5 years ago by ▴ 150
0
votes
0
replies
888
views
Job: Postdoctoral Research Fellow position in Molecular Biology
methylation nanopore-sequencing RNA
updated 2.2 years ago by 45k • written 4.5 years ago by • 0
0
votes
0
replies
709
views
How to use combat in order to remove batch effects?
RNA-Seq
updated 4.5 years ago by 13k • written 4.5 years ago by ▴ 10
2
votes
1
reply
2.8k
views
pv4 values interpretation
pv4 vcf strand bias baseQbias SNP
updated 4.5 years ago by • 0 • written 9.1 years ago by ▴ 30
1
vote
0
replies
578
views
hmmsearch result query name problem
alignment sequence
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 10
5
votes
7
replies
2.2k
views
Estimate running time of a orthoFinder
gene bacteria genome
updated 4.5 years ago by 56k • written 4.6 years ago by ★ 2.8k
4
votes
8
replies
1.3k
views
How to interpret one region of gene with much higher RNASeq coverage than other regions?
RNA-Seq
4.5 years ago by CephBirk ▴ 20
0
votes
0
replies
827
views
Reference species for Augustus
augustus
4.5 years ago by henry-keen ▴ 50
1
vote
15
replies
3.1k
views
Picard ValidateSamFile Error: "ValidateSamFile Value was put into PairInfoMap more than once"
samtools bam sam picard alignment
4.5 years ago by stephen.johnson.online • 0
5
votes
6
replies
3.3k
views
Minor allele count report with --freq count in PLINK2
PLINK MAF
updated 4.5 years ago by 11k • written 4.5 years ago by ▴ 10
7
votes
13
replies
4.7k
views
bcftools +fill-tag does not work in loop
bcftools plugin +fill-tags loops
updated 4.5 years ago by 3.1k • written 4.5 years ago by ▴ 30
0
votes
2
replies
2.6k
views
How to make SBGNview accepts custom sbgn input or kegg pathway? ID mapping tables between gene IDs and SBGN file glyph IDs.
sbgnview pathview sbgn metabolomics
updated 2.3 years ago by 45k • written 4.5 years ago by ▴ 190
0
votes
0
replies
660
views
Looking for VCF files and clinical data for cancer (prostate or cll or breast)
vcf cancer somatic mutations access to data
4.5 years ago by ansakim20 ▴ 10
1
vote
6
replies
2.4k
views
Comparing two gene lists for orthologs
orthologs biopython
updated 4.5 years ago by 20 • written 9.2 years ago by ▴ 40
0
votes
0
replies
488
views
Aligning divergent mitochondrial genomes - software recommendations?
alignment genome
4.5 years ago by ryan.gawryluk • 0
0
votes
2
replies
1.0k
views
demultiplexing "undetermined" ddrad data
ddRAD
4.5 years ago by kulzer • 0
0
votes
2
replies
723
views
a simple question about file permissions
SLURM cluster operating system
4.5 years ago by Bogdan ★ 1.4k
8
votes
11
replies
2.6k
views
Getting standard 12-column format for a list of genes
genome
updated 4.5 years ago by 22k • written 4.5 years ago by ★ 4.4k
0
votes
9
replies
1.4k
views
The maximum number of peaks in a ChIP-seq data (bigWig format)
ChIP-Seq
4.5 years ago by prgrmmr70 • 0
0
votes
1
reply
686
views
How to find if sequences perfectly overlap
biopython pairwise2
4.5 years ago by gero.knittel ▴ 10
0
votes
0
replies
455
views
Using Maker to map foward annotations from reference gff
annotation
4.5 years ago by robert.murphy ▴ 110
121,912 results • Page 699 of 2439
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Getting VCF file for the 1000 genome project with rsid
Answer: Different UMAP for batch correction in R and Pytho
Answer: Different UMAP for batch correction in R and Pytho
Answer: Different UMAP for batch correction in R and Pytho
A: How to extract reads with no INDEL?
Answer: Different UMAP for batch correction in R and Pytho
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Recent Replies
Comment: Tried building a compact sequence format with 4-bit storage by Alex Reynolds 36k
In addition to looking at other tools as a baseline: https://en.wikipedia.org/wiki/Compression_of_genomic_sequencing_data maybe also look i…
Comment: Different UMAP for batch correction in R and Pytho by Madiha ▴ 10
Thanks, António for a helpful, detailed response. I didn't take into consideration that the plotting order of cells from each batch can be …
Comment: [vg giraffe] Unable to add read group to BAM file by saruman • 0
It seems that using the following format fixes the problem: --read-group "1 SM:HG002 LB:lib1 PL:illumina PU:unit1" As shown below: …
Comment: Developing a genomics ML model using bytes? by dariober 15k
> what if we can use the bytes to develop a model? My understanding is that the OP is considering building a model using the sequences in …
Comment: WGCNA package in R: dendogram plot error by RJ • 0
You might had delete the outliers from the expression table but then the traits data.frame doesn't match with expression table dimensions.
Comment: miRNA low mapping ratings by Ant ▴ 50
No, it's a personal dataset. I haven’t seen the link, but if I understand correctly, it's not possible to use the software for free, right?
Comment: miRNA low mapping ratings by GenoMax 153k
So this is a public dataset? QIAseq miRNA libraries may require special handling. Have you seen --> https://resources.qiagenbioinformatics.…
Comment: Trouble when installing arb by GenoMax 153k
Are you referring to software found here --> http://download.arb-home.de/release/latest/ ? If so why are you installing the source. Authors…
Comment: Hifiasm is getting killed while trying to assemble a genome by GenoMax 153k
All valid points. This is a SRA dataset. If it is covered by a publication hopefully it is not a bad one. @Pranav if you can post the SRA a…
Answer: Different UMAP for batch correction in R and Pytho by antonioggsousa 3.4k
Hi, I'm mostly an R user, but the codes you presented look correct to me. The two UMAP projections *"look too similar to be different"*, …
Answer: How to properly assemble phage genomes? by Joe 22k
This might help: https://millardlab.org/lab-members/alumni/lucy-gannon/lucys-beginner-guide-to-bacteriophage-genome-assembly/
Comment: RNA-SEQ where only a subset of genes is of interest by piffelpaff • 0
Thanks for your reply. Yes it's single-cell and we're talking about roughly 30 pre-selected genes. I see. I was rather referring to the d…
Answer: Best set of tools / workflows for predicting the biosynthesis pathways of comple by Joe 22k
This may not be exactly what you're looking for (kind of the other way around, predicting synthetic clusters from genes rather than the pro…
Comment: Developing a genomics ML model using bytes? by ATpoint 89k
How is this different from https://www.biostars.org/p/9615062/
Comment: Shift in RNA 3' position, Term-Seq vs RNASeq by npb27 ▴ 20
Hi thanks for your answer Interesting idea about ribosome length, although I can't think why this should affect the apparent 3' position b…
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