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GenomeStudio in a cloud service
genomestudio aws
updated 4.4 years ago by 153k • written 4.4 years ago by • 0
1
vote
1
reply
1.2k
views
Correcting for batch effect in survival data
survival batch-effect
updated 13 months ago by 45k • written 4.4 years ago by ▴ 300
2
votes
5
replies
8.4k
views
Error in loadNamespace(name) : there is no package called ‘shiny’
MetaQc R R-studio Geodatasets MetaOmics
4.4 years ago by xxxxxxxx ▴ 20
8
votes
3
replies
1.8k
views
Getting libType without running quantification with Salmon
strandness salmon rnaseq python strand
updated 4.4 years ago by 7.1k • written 4.4 years ago by ▴ 140
0
votes
2
replies
856
views
Genome search on FTP NCBI
NCBI
4.4 years ago by Debut ▴ 20
7
votes
12
replies
2.6k
views
Failing to run tblastn
tblstn blast
updated 4.4 years ago by 153k • written 4.4 years ago by ▴ 70
0
votes
0
replies
635
views
Snakemake only reads the target rule and not the other rules
Snakemake
4.4 years ago by rudylu.monica • 0
0
votes
2
replies
1.1k
views
How to do damage calibration after vg map
vgtool vg PMD aDNA
4.4 years ago by puddingmeow516 ▴ 10
0
votes
0
replies
806
views
Why ABSOLUTE calculate CCF=NA?
ABSOLUTE
4.4 years ago by Laven9 • 0
1
vote
1
reply
1.0k
views
Detecting Human Contamination in Low Coverage NGS sample
verifybamid CalculateContamination
4.4 years ago by igorm ▴ 20
2
votes
3
replies
1.4k
views
Is there a way to include not conda package/programs to snakemake environment?
Non-Conda_packages Snakemake
4.4 years ago by lmlukoseviciute ▴ 60
0
votes
0
replies
529
views
transition plot between chromatin states from non-tumour to tumour sample
Gmisc R
updated 2.5 years ago by 45k • written 4.4 years ago by ▴ 30
0
votes
0
replies
802
views
remove from mummerplot some contigs
mummerplot mummer
4.4 years ago by shinken123 ▴ 150
0
votes
0
replies
722
views
using TREEMM for identification of bipartite motifs in promoter sequences
CLUSTERS TREEMM PROMOTER
4.4 years ago by madhujamano • 0
6
votes
8
replies
2.2k
views
Diseases related pathways
pathways wikipathway kegg reactome
updated 4.4 years ago by ▴ 580 • written 4.7 years ago by ▴ 80
1
vote
2
replies
2.1k
views
Understanding why `Design matrix not of full rank. The following coefficients not estimable` during GLM
edgeR design-matrix differential glm offtopic
updated 4.4 years ago by 89k • written 4.4 years ago by ▴ 750
0
votes
0
replies
743
views
PAML (CODEML) with 0 branch lengths
PAML codeml
4.4 years ago by DNAlias ▴ 40
1
vote
8
replies
2.3k
views
DESeq2 comparison two cell types and two genotypes
DESEQ2
updated 4.4 years ago by ★ 1.9k • written 4.4 years ago by • 0
0
votes
0
replies
536
views
Extracting Position-specific di-amino acid propensity(PSTAAP) features
protein features propensity sequences
4.4 years ago by suresh.wrc • 0
1
vote
0
replies
598
views
The best way to find cell differentiation path
differentiation fate biology fibroblasts scRNA-seq
4.4 years ago by fifty_fifty ▴ 90
3
votes
2
replies
1.3k
views
Plink/VCFTools pairwise LD is always 1
disequilibrium LD plink linkage vcftools
4.4 years ago by pmc.sa ▴ 40
0
votes
1
reply
796
views
modify name field from genbank file
gb genebank gene GATU
updated 4.4 years ago by ★ 30k • written 4.4 years ago by • 0
0
votes
5
replies
1.9k
views
Consensus deduplication issues with non-matching/'slippy' primers?
DNA-seq deduplication
updated 4.4 years ago by 22k • written 4.4 years ago by ▴ 110
0
votes
0
replies
480
views
RNA sequencing analysis pipeline for micro RNA mutants
sequencing RNA
4.4 years ago by aranyak111 • 0
4
votes
5
replies
2.7k
views
how to understand the P value of the Deseq2 results
statistics p_value DEseq2
updated 4.4 years ago by ★ 2.6k • written 4.4 years ago by ▴ 130
0
votes
1
reply
897
views
Retrieving One-to-One Orthologs of Unprocessed cDNAs
sequencing orthologs
updated 4.4 years ago by 153k • written 4.4 years ago by • 0
5
votes
2
replies
2.2k
views
Is it technically correct to eliminate branches with low bootstrap ?
phylogenetics
updated 4.4 years ago by ★ 30k • written 4.4 years ago by • 0
1
vote
1
reply
1.2k
views
Remove duplicate SNPs by allele frequency in PLINK
QC plink
updated 4.4 years ago by 11k • written 4.4 years ago by • 0
0
votes
3
replies
1000
views
Possibility of using 10x Genomics reads from another individual
genome-assembly
updated 4.4 years ago by 153k • written 4.4 years ago by • 0
0
votes
3
replies
1.9k
views
Abnormal GC content in Whole Exome Sequencing Sample after alignment
library WES GC Sequencing FASTQC
updated 3.9 years ago by • 0 • written 4.4 years ago by • 0
0
votes
2
replies
1.4k
views
Find the publication of the dataset available in NCBI's SRA Library
SRA 16s NCBI
updated 4.4 years ago by 153k • written 4.4 years ago by ▴ 50
6
votes
12
replies
3.9k
views
BAI index format
BAI index BAM CSI
4.4 years ago by maxrwjones ▴ 60
4
votes
10
replies
7.2k
views
7 follow
Unable to find adapter seq using Fastp
sequencing sequence assembly software error fastp
updated 4.4 years ago by ★ 2.9k • written 6.9 years ago by • 0
4
votes
7
replies
2.3k
views
Variable numbers of Reads. I'm lost
Nanopore featureCount Alignment Sequencing Reads
updated 4.4 years ago by 48k • written 4.4 years ago by • 0
2
votes
3
replies
2.3k
views
Using VEP custom on ClinVar error - Couldn't find index.
vep custom ensembl clinvar
4.4 years ago by milwaukee • 0
2
votes
2
replies
3.4k
views
get count matrix from bam files
bam ATAC-seq
updated 2.3 years ago by 45k • written 4.4 years ago by ▴ 70
0
votes
1
reply
761
views
Array express microarray single channel agilent data only contain Green.DerivedSignal values??
microarray r
updated 4.4 years ago by 89k • written 4.4 years ago by ▴ 30
4
votes
1
reply
1.3k
views
How to trim alignments in a BAM file to a restricted genomic window?
bam alignment
updated 4.4 years ago by 166k • written 4.4 years ago by ▴ 90
6
votes
5
replies
1.6k
views
6 follow
Remove 2nd colon and rest of the values in a dataframe using R/ Unix
coordinates SNP Unix R
updated 4.4 years ago by 12k • written 4.4 years ago by ▴ 70
3
votes
4
replies
2.8k
views
FeatureCounts total alignment = 0. Can you help me please
Nanopore RNAseq Bam featureCounts NGS
updated 4.4 years ago by 103k • written 4.4 years ago by • 0
4
votes
5
replies
2.0k
views
De novo assembly of chloroplast genome
Scaffolding Illumina assembly
updated 4.4 years ago by ★ 1.8k • written 4.4 years ago by ▴ 20
0
votes
2
replies
2.1k
views
FastQC per sequence GC content
FastQC GCcontent qualitycontrol
4.4 years ago by jhy ▴ 10
1
vote
2
replies
1.1k
views
Ensembl fasta DNA data
ensembl genome mitochondria
4.4 years ago by kb_93 ▴ 10
2
votes
1
reply
770
views
Reconstructing an incomplete transcript of interest
RNAseq transcriptomics NGS
updated 4.4 years ago by ★ 1.8k • written 4.4 years ago by ▴ 30
0
votes
24
replies
4.9k
views
converting spaces to tabs in gtf files
NCBI
4.4 years ago by storm1907 ▴ 30
0
votes
0
replies
583
views
correlation of WGBS dataset and RNAseq dataset
transcription methylation
4.4 years ago by frylhc • 0
0
votes
1
reply
924
views
Using nhmmer to identify gene members of a superfamily
genes nhmmer profilehmmer hmmer
updated 3.6 years ago by • 0 • written 4.4 years ago by ▴ 60
0
votes
4
replies
1.3k
views
Add all non overlapping genes/transcripts from one gtf to another with bedtools intersect
bedtools annotation gtf
4.4 years ago by robert.murphy ▴ 110
10
votes
8
replies
5.1k
views
Can Plink Be Used For The Analysis Of A Bacterial Dataset?
plink
updated 4.4 years ago by ▴ 10 • written 12.3 years ago by ▴ 40
0
votes
1
reply
2.3k
views
What is the best way to perform a PCA on .vcf of closely related bacteria?
variant-calling
updated 18 months ago by 45k • written 4.5 years ago by ▴ 10
121,890 results • Page 663 of 2438
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Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Answer: Structural Variant identification on pangenome graphs
Answer: Stringtie de novo VS reference guided (-G)
Answer: Yeast reference-based genome assembly
How to Identify Conserved 21-mers Across TE Insertions in Drosophila?
How to Identify Conserved 21-mers Across TE Insertions in Drosophila?
Answer: Rna-seq data
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Recent Replies
Comment: magpurify errors by shevch2009 ▴ 20
I have checked with my eyes, and I didn't find it, I have only one contig that starts with k127_458 .... but the name is different - k127_4…
Comment: Yeast reference-based genome assembly by Michael 56k
So, you aren't sure about the exact species? Then you might want to be careful with reference-based assembly in general. I recommend the fo…
Comment: Structural Variant identification on pangenome graphs by Panos ★ 1.8k
That's a very comprehensive list! Thanks for sharing! `minigraph` better suits my needs because all I need is SVs for my genomes. As far a…
Comment: Yeast reference-based genome assembly by amy967107 • 0
I have ~2.01 Gb of ONT data and the target genome is ~20–23 Mb (90–100× coverage). My ONT read N50 is ~3.8 kb, so contiguity may be limited…
Comment: Yeast reference-based genome assembly by amy967107 • 0
This is a yeast strain (probably Rhodotorula spp.) and I'm trying to assemble the entire genome from nanopore reads using a reference-based…
Answer: Yeast reference-based genome assembly by Michael 56k
The new [hifiassm ONT][1] may be all you need for getting a good assembly. I would not recommend LRSDAY, except for its annotation part (wh…
Comment: magpurify errors by Mensur Dlakic ★ 30k
By the way, these errors are not unique. If you look through the `magpurify` GitHub issues, both types have been reported already. - https…
Comment: magpurify errors by Mensur Dlakic ★ 30k
There is absolutely no chance that a contig labeled `k127_4584534` doesn't exist in your fasta files. These names are not made up out of th…
Comment: magpurify errors by shevch2009 ▴ 20
Strange but there are no such headers or contig names in my fasta files
Comment: replace gene names in gff file by Juke34 9.3k
Yes the --prefix Option exists. There is no count per chromosome. You can do it by splitting your input and analyse one sequence at a time…
Comment: Variant analysis for mouse WES by GenoMax 153k
You could open a new issue and ask the developers of `maftools` if this was something they can add.
Comment: How to Identify Conserved 21-mers Across TE Insertions in Drosophila? by GenoMax 153k
Do you have the locations/sequence of the regions you are interested in?
Comment: magpurify errors by shevch2009 ▴ 20
Thank you
Comment: magpurify errors by Mensur Dlakic ★ 30k
To me that sounds like an error in sequence header formatting. Maybe some contig headers are repeated? Or their sequences are short or miss…
Comment: magpurify errors by shevch2009 ▴ 20
Thanks What about phylo-markers module error, I tried to look for it :) But haven't found anything. And why it's not working for some but …
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