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5
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9
replies
2.0k
views
How can I extract mostly expressed genes from a series matrix?
WGCNA R RNA-seq
4.5 years ago by microorganism_001 ▴ 30
1
vote
3
replies
1.4k
views
Downloading data from 1000Genomes
1000Genomes vcf
updated 4.5 years ago by 12k • written 4.5 years ago by ▴ 20
0
votes
4
replies
1.7k
views
> 90% samples, DP > 10
VCF R DP
updated 4.5 years ago by ▴ 480 • written 4.5 years ago by ▴ 110
6
votes
4
replies
2.9k
views
Genome annotation file GFF3 and GTF same? interchangeable?
GTF GFF3 NGS ANNOTATION
4.5 years ago by SKY ▴ 60
0
votes
3
replies
1.1k
views
Forum: what for masters?
microbio masters
updated 4.5 years ago by ★ 2.9k • written 4.5 years ago by • 0
0
votes
1
reply
865
views
PCA and bar plot in Tripal
tripal plots
updated 4.5 years ago by 12k • written 4.5 years ago by ▴ 120
0
votes
2
replies
1.1k
views
How to convert RNAhybrid output to data frame
RNAhybrid
updated 4.5 years ago by 56k • written 4.5 years ago by • 0
2
votes
2
replies
1.7k
views
Using DAVID Web Service to classify genes into functional groups
DAVID-Web-Service david
4.5 years ago by langziv ▴ 70
0
votes
0
replies
1.0k
views
GATK MUTECT2
gatk mutect2
updated 2.7 years ago by 45k • written 4.5 years ago by • 0
0
votes
1
reply
638
views
how to removed the nucleotides from a fastq file (single-end) in conditional
PAS-seq
updated 4.5 years ago by ★ 2.9k • written 4.5 years ago by ▴ 30
0
votes
3
replies
1.9k
views
Mapping fastq files to reference genome
reference-genome mapping fastq
updated 2.2 years ago by 45k • written 4.5 years ago by ▴ 180
1
vote
4
replies
1.4k
views
Header conflicts in concatenated FASTQ file?
FASTQ RNA-seq concatenate
4.5 years ago by Dunois ★ 2.9k
0
votes
1
reply
905
views
samtools depth vs Rsamtools pileup
Samtools RSamtools Bioconductor R
4.5 years ago by chasem ▴ 50
6
votes
4
replies
2.6k
views
how to removed the first two nucleotides from a fastq file (single-end)
CGAE-seq fastq
updated 4.5 years ago by 21k • written 4.5 years ago by ▴ 30
0
votes
0
replies
841
views
Truncated sam File from Resfinder Database in MGmapper
mapping
4.5 years ago by hafiz.talhamalik ▴ 350
0
votes
1
reply
1.0k
views
Query regarding WGCNA module formation
WGCNA RNA-seq
updated 4.5 years ago by 22k • written 4.5 years ago by ▴ 30
0
votes
3
replies
1.0k
views
function annotation
GO
updated 4.5 years ago by ★ 2.9k • written 4.5 years ago by • 0
0
votes
0
replies
641
views
how to annotate mapping peaks within a defined genomic region？
piRNA genome RNA-seq annotation
4.5 years ago by tianshenbio ▴ 190
1
vote
2
replies
2.2k
views
How to print the header of bed file and the lines that belong to chromosome 2
fastq Bed_files fasta Bash
updated 4.4 years ago by 45k • written 4.5 years ago by ▴ 20
0
votes
1
reply
843
views
Best graph/plot to convey gene expression differences across time?
graph plot Gene Expression R
updated 4.5 years ago by ★ 1.7k • written 4.5 years ago by • 0
3
votes
5
replies
2.0k
views
How to use lapply to extract taxonomic information in my species list?
R
4.5 years ago by DNAngel ▴ 260
0
votes
2
replies
1.3k
views
Forum: Study Materials
learning study materials
4.5 years ago by AHa • 0
1
vote
2
replies
1.3k
views
Duplicate markers
duplicate plink markers
4.3 years ago by Alexandra ▴ 20
0
votes
3
replies
1.6k
views
SOAPaligner- 2bwt-builder segmentation fault
soapaligner c linux
updated 4.4 years ago by 45k • written 4.5 years ago by • 0
0
votes
3
replies
2.0k
views
How to perform GO enrichment for non-model species
non-model-species Gene-Ontology GO-enrichment
4.4 years ago by Kumar ▴ 170
0
votes
0
replies
1.3k
views
What is the file .mums created by mummer ?
Mummer Alignment Mummerplot Genome
updated 4.4 years ago by 45k • written 4.5 years ago by ▴ 30
1
vote
0
replies
948
views
Discussion on binning multiple metagenomes at the same time?
binning metagenomics mags
4.5 years ago by O.rka ▴ 750
6
votes
9
replies
3.6k
views
Preparing Target Data
PGS PRS PRSice
updated 4.5 years ago by ★ 4.8k • written 4.5 years ago by ▴ 20
1
vote
6
replies
2.0k
views
Anyone can help me to interpret this ClonalFrameML output?
Recombination ClonalFrameML Phylogenies
updated 3.8 years ago by 22k • written 4.5 years ago by • 0
0
votes
2
replies
962
views
How to get domain/kingdom name in a table of taxid in R tidyverse?
R
4.5 years ago by DNAngel ▴ 260
2
votes
4
replies
1.7k
views
Rsamtools: get nucleotide of read ID X at position P
rsamtools
4.5 years ago by francois ▴ 90
1
vote
2
replies
1.3k
views
Get by-strand base counts at position from cram file
igv cram count strand details
4.5 years ago by davenomiddlenamecurtis ▴ 20
3
votes
5
replies
1.2k
views
Developing algorithms
Microbial genomics
updated 4.5 years ago by 22k • written 4.5 years ago by • 0
1
vote
1
reply
1.1k
views
How to access specific gene data from the NCBI Gene database with Biopython
Biopython
updated 4.5 years ago by 103k • written 4.5 years ago by • 0
4
votes
3
replies
6.0k
views
kraken2 unclassified output does not work with paired reads?
Kraken2
updated 4.5 years ago by 103k • written 4.5 years ago by ▴ 260
4
votes
3
replies
1.5k
views
What do the samtools column names mean
NGS samtools
updated 4.5 years ago by 45k • written 4.5 years ago by • 0
0
votes
6
replies
2.5k
views
How to identify snps in gene
snp identification
4.5 years ago by Ak ▴ 60
1
vote
1
reply
764
views
Extract co-ordinate for iCLIP data?
sequencing linux RNA
updated 4.5 years ago by 103k • written 4.5 years ago by ▴ 130
2
votes
1
reply
1.9k
views
Preparing data for kinship calculations
PRUNING VCF PLINK2 KING
updated 4.5 years ago by 45k • written 4.5 years ago by ▴ 110
2
votes
3
replies
1.3k
views
plotting stacked bar plot with different number and kinds of variables
stackedbarplot ggplot
4.5 years ago by Curls ▴ 40
1
vote
6
replies
3.4k
views
how to implement a database with several FASTA files
Database NCBI FASTA
updated 4.5 years ago by 103k • written 4.5 years ago by ▴ 20
1
vote
3
replies
2.7k
views
PAM250 and BLOSUM62 probability of substitution matrices
blosum matrix pam
updated 4.5 years ago by ★ 30k • written 4.5 years ago by • 0
0
votes
0
replies
789
views
Goseq - Pwf: Error In If (Hi <= Low) { : Missing Value Where True/False Needed
r goseq ontology Gene GO
updated 4.5 years ago by 45k • written 4.5 years ago by ▴ 30
0
votes
0
replies
698
views
How to derive an inverse simpson index(alpha diversity) from the phylosift results
phylosift alpha diversity
4.5 years ago by tmfdk0819 • 0
0
votes
2
replies
1.2k
views
Clustering artefacts when processing single-nucleus RNAseq
single-cell RNA Seurat UMAP
4.5 years ago by MikeV ▴ 10
4
votes
8
replies
9.3k
views
Help with designing limma contrast matrix
limma software error
updated 2.7 years ago by ★ 90k • written 7.7 years ago by ★ 4.4k
1
vote
4
replies
2.9k
views
deeptools 3.5 plotCorrelation
ChIP-Seq sequencing plotCorrelation next-gen deeptools
updated 4.5 years ago by 9.0k • written 4.5 years ago by ▴ 20
4
votes
11
replies
11k
views
7 follow
Single cell DEG analysis. Wildly different results from different FindMarkers test
rna-seq seurat
updated 4.5 years ago by 45k • written 5.3 years ago by ▴ 20
0
votes
5
replies
2.2k
views
TCGA data Query (GDCquery): external_gene_name " are missing
TCGABiolinks R TCGA
updated 2.7 years ago by 45k • written 4.5 years ago by • 0
7
votes
1
reply
1.5k
views
Herald: The Biostar Herald for Wednesday, June 02, 2021
herald
updated 4.5 years ago by 103k • written 4.5 years ago by 3.7k
122,199 results • Page 646 of 2444
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Answer: Midpoint rooting IQTREE newick file moves node support around
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Answer: Can i use orthofinder for small protein datasets and not full proteome?
Comment: Comparison of different RNAseq data sets
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Comment: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
You can check the read lengths of each file to determine which one is the R1 and which is the R2. Also, check the 10x protocol version they…
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!
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