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400 results • Page 4 of 8
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0
votes
4
replies
287
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Genbank File Format
gbkformat
13 days ago by alenew.am • 0
0
votes
0
replies
256
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma ArrayExpress DifferentialExpression GEOquery
14 days ago by SSSJec • 0
0
votes
3
replies
239
views
Software to separate reads from different individuals
software development nanopore
updated 14 days ago by 142k • written 14 days ago by ▴ 20
0
votes
2
replies
314
views
How to update R on ubuntu
installation update R apt-get
14 days ago by Bosberg ▴ 50
0
votes
0
replies
119
views
LEfSe
LEfSe
14 days ago by benkosta • 0
0
votes
0
replies
96
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq DEXSeqDataSet SGSeq
14 days ago by Sara ▴ 30
0
votes
2
replies
176
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression DEG model
14 days ago by Lluís R. ★ 1.2k
0
votes
0
replies
110
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics Mass-spectrometry Proteins
updated 8 hours ago by 43k • written 14 days ago by ▴ 30
0
votes
2
replies
222
views
What should I consider as FASTA for dataset?
PDB FASTA
14 days ago by Nafi • 0
0
votes
0
replies
601
views
Differential accessibility using DiffBinf
diffbind
15 days ago by Shloka • 0
0
votes
0
replies
105
views
vg call vs vg surject
vg variation graphs
updated 14 days ago by 142k • written 15 days ago by • 0
0
votes
1
reply
228
views
Finding batch and outlayers
Pca
updated 14 days ago by ▴ 460 • written 15 days ago by • 0
2
votes
2
replies
223
views
PDB related issue
rcsb pdb
updated 15 days ago by ▴ 580 • written 15 days ago by • 0
0
votes
9
replies
2.6k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome base-calling fastq nanopore
updated 15 days ago by 43k • written 8 months ago by • 0
1
vote
2
replies
259
views
Downloading full alignments from Pfam
pfam
8 days ago by bef1 • 0
0
votes
0
replies
136
views
adjusting for confounders in LMER in R
confounders LMER R
updated 14 days ago by 14k • written 15 days ago by ▴ 20
1
vote
3
replies
359
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 15 days ago by 82k • written 16 days ago by ▴ 10
0
votes
0
replies
151
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
16 days ago by tnminh89 ▴ 10
0
votes
0
replies
157
views
Filter low express genes in microarray data
microarray
16 days ago by Chris ▴ 280
0
votes
0
replies
582
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell Spatial-Transcriptomics
17 days ago by biocellbio • 0
0
votes
0
replies
218
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes vcf phasing
17 days ago by HarperReed • 0
1
vote
0
replies
169
views
Simulation of label-free bottom-up proteomics expression dataset
label-free bottom-up lc-ms proteomics
17 days ago by KABILAN ▴ 70
0
votes
0
replies
188
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics phylogenetic
updated 17 days ago by 43k • written 18 days ago by • 0
0
votes
0
replies
189
views
RNA-seq: full length gene
RNA-seq
updated 17 days ago by 43k • written 18 days ago by • 0
0
votes
0
replies
169
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly phased Haplotype Annotation
18 days ago by turcoa1 • 0
0
votes
0
replies
180
views
Designing single-stable RNA molecules
structure RNA
18 days ago by Edna • 0
0
votes
0
replies
192
views
How to visualize/predict the final transcript from Delly output?
WGS DELLY
18 days ago by simplitia ▴ 130
1
vote
1
reply
260
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing housekeeping Single-cell normalization
updated 18 days ago by 82k • written 18 days ago by • 0
0
votes
0
replies
175
views
How to calculate correlation coefficient for chipseq?
chipseq bigwigsummary deeptools correlation
2 hours ago by Emily ▴ 20
1
vote
0
replies
189
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds kaks VCF
18 days ago by rohitsatyam102 ▴ 860
0
votes
0
replies
171
views
how to read graph_test output of monocle 3
monocle3
18 days ago by synat.keam ▴ 100
0
votes
1
reply
529
views
GAPIT p-value significance threshold
GAPIT p-value GWAS
updated 18 days ago by • 0 • written 5 months ago by • 0
0
votes
0
replies
169
views
Why not use iBAQ for calculating differential abundance of proteins?
protein maxquant
18 days ago by Aspire ▴ 330
0
votes
4
replies
400
views
Highest variable features in single cell data
single-cell
6 days ago by carolofharvest ▴ 40
1
vote
3
replies
439
views
PCA plot
DESeq2 PCAplot
updated 15 days ago by 4.2k • written 19 days ago by ▴ 10
0
votes
0
replies
165
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein pdb alpha-carbon
19 days ago by 4fzcgueyp5 • 0
0
votes
2
replies
306
views
Annovar using R package
Annovar gnomAD R
18 days ago by DKA ▴ 40
0
votes
5
replies
430
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 18 days ago by 142k • written 19 days ago by ▴ 90
0
votes
0
replies
163
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA GDCprepare
updated 19 days ago by 43k • written 19 days ago by • 0
0
votes
0
replies
325
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome PGAP NCBI roary Prokka
19 days ago by pramach1 ▴ 40
0
votes
1
reply
200
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate GEMMA GWAS
updated 19 days ago by • 0 • written 19 days ago by • 0
0
votes
0
replies
163
views
Sequence BLAST in plus/minus and plus/plus
blast CRISPR strand sequencing
19 days ago by salias • 0
0
votes
5
replies
448
views
different FeatureCounts output for the same data
fpkm Counts Rsubread rna-seq
updated 16 days ago by 100k • written 19 days ago by ▴ 10
0
votes
0
replies
138
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq single-cell suppa alternative-splicing
updated 19 days ago by 43k • written 19 days ago by • 0
1
vote
2
replies
276
views
alignment result
RNA-seq samtools hisat2
19 days ago by ahmad.sajad4541 • 0
0
votes
0
replies
136
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile scvelo scipy annData numpy
20 days ago by Kash ▴ 110
0
votes
1
reply
186
views
How to solve this RoseTTAFold colaboratory error?
modeling Google Colaboratory RoseTTAFold protein
updated 20 days ago by ★ 27k • written 20 days ago by • 0
2
votes
2
replies
330
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein FASTA alignment
updated 19 days ago by 43k • written 20 days ago by ▴ 140
2
votes
9
replies
928
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 20 days ago by 4.2k • written 7 months ago by • 0
0
votes
11
replies
692
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
18 days ago by atowns21 • 0
400 results • Page 4 of 8
Recent Votes
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
A: How can I convert -log10 (p-value) to p-value?
Comment: What does the 'E%' represent in BUSCO results?
Answer: What does the 'E%' represent in BUSCO results?
Answer: Combine Two Affymetrix Datasets With Same Platform
Comment: Kraken2 database
Comment: How does gene length effect the number of reads mapped
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Recent Replies
Answer: Snakemake wrapper issue by Wei-Chen Pan • 0
Hi, did you solve your problem ? I also encounter same issue but it's `wrapper:"v3.9.0/bio/picard/mergevcfs"`. In my log file, it said:…
Comment: What does the 'E%' represent in BUSCO results? by Philipp Bayer 8.5k
No worries! I found the commit with the maths too: https://gitlab.com/ezlab/busco/-/blame/master/src/busco/busco_tools/hmmer.py?page=2#L135…
Comment: What does the 'E%' represent in BUSCO results? by 林明德 • 0
Thank you for your answer! It really helped me resolve a doubt!
Answer: What does the 'E%' represent in BUSCO results? by Philipp Bayer 8.5k
Ah your edit solved this. 50 BUSCOs contain internal stop codons, indicating they might be erroneous gene models, or the genes themselves a…
Answer: MGLTools does not work in windows 11 by Ashfaq • 0
In my case, I did not see iGPU. There is only one option, Intel UHD Graphics. What I need to do?
Comment: What does the 'E%' represent in BUSCO results? by Philipp Bayer 8.5k
funny enough i tried the same thing (i've used BUSCO heaps times but never saw the E:! even the manual lists 'C:89.0%[S:85.8%,D:3.2%],F:6.9…
Comment: What does the 'E%' represent in BUSCO results? by GenoMax 142k
According to ChatGPT: In BUSCO, the "E" category represents "End" or "Endof" gene fragments. These are orthologous groups for which the ge…
Comment: Help with IGV abbreviation by GeneC • 0
Thank you for the link and details
Comment: Help with IGV abbreviation by GeneC • 0
Thank you very much for helping with the details.
Comment: How does gene length effect the number of reads mapped by Chen • 0
thank you :)
Answer: Filtering based on alternate allelic balance by Arton • 0
I found the answer when using bcftools. Is there is a way to do this with FilterVcf? bcftools filter --include '(FMT/AD[0:1])/(FMT/A…
Comment: Help with IGV abbreviation by GenoMax 142k
Those are SAM format fields. Check section 1.4 here: https://samtools.github.io/hts-specs/SAMv1.pdf > 1:2114:12111:13792 That is part of …
Answer: Help with IGV abbreviation by Mathew ▴ 130
Hi, here is a breakdown of each part that you asked about: **flag 99**: This indicates various properties of the read alignment. In this c…
Comment: Kraken2 database by Mathew ▴ 130
I don't see any databases with just pathogenic bacteria genomes from just a quick search, I would imagine that using the Standard-16 databa…
Comment: Galaxy StringTie error by Mathew ▴ 130
I am not sure if this is true for Galaxy, but when I code in Python, SyntaxWarning: invalid escape sequence '' occurs when you want to add …
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