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182 results • Page 3 of 4
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0
votes
1
reply
117
views
How to hide label in layout file of MCscan (python version)
MCscan
updated 6 days ago by 142k • written 7 days ago by • 0
0
votes
1
reply
617
views
Illumina methylation EPIC V2 array
ewas methylation enrichment missMethyl EPIC
updated 6 days ago by ▴ 40 • written 8 months ago by • 0
0
votes
3
replies
222
views
GATK Structural Variants Pipeline - Steps
SV GATK Variant-Calling
updated 6 days ago by 44k • written 7 days ago by ▴ 20
0
votes
0
replies
110
views
transcriptome annotation
annotation trinity transcriptome
updated 6 days ago by 44k • written 7 days ago by • 0
0
votes
0
replies
104
views
Is it possible to keep gene_id and gene_name columns using Seurat::Read10X?
Seurat single-cell scRNA-seq
updated 6 days ago by 44k • written 7 days ago by ▴ 20
0
votes
5
replies
249
views
Why most genes have high padj values
RNA-seq DEG
updated 6 days ago by 44k • written 7 days ago by • 0
0
votes
2
replies
220
views
How to generate an Upset plot in R to plot the shared variants between cell free DNA samples
r Upset
6 days ago by sainavyav22 • 0
0
votes
2
replies
290
views
How can I calculate the OS of each patient?
overall-survival
6 days ago by Pedro • 0
0
votes
0
replies
104
views
News: Online course: Network analysis in Systems Biology with R/Bioconductor
Bioconductor Systems-Biology Network-Analysis R
updated 6 days ago by 44k • written 6 days ago by ★ 2.5k
0
votes
0
replies
183
views
How to deal with possibly important predictors omitted during the building of an OLS multivariant linear regression model?
multivariant-linear-regression
updated 6 days ago by 44k • written 7 days ago by ▴ 20
0
votes
0
replies
125
views
problems in installing rDock
rDock
updated 6 days ago by 44k • written 8 days ago by • 0
0
votes
3
replies
266
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 6 days ago by ▴ 130 • written 7 days ago by ▴ 30
0
votes
1
reply
124
views
Nextflow docker: Error response from daemon
sarek gatk4 docker nextflow
updated 6 days ago by 162k • written 6 days ago by ▴ 200
0
votes
0
replies
95
views
How to recover the entire sequence from all_contig_annotations.csv?
VDJ single-cell TCR-seq cellranger 10x
6 days ago by dawnyipingzou • 0
0
votes
0
replies
92
views
Calculated LAI is too large
annotation LAI assembly TE genome
6 days ago by Yao ▴ 30
0
votes
0
replies
93
views
Last step of metagenome analysis before visualization
metagenome python analyis
5 days ago by Ayda Ecem • 0
0
votes
1
reply
140
views
DRAGEN gVCF files and joint calling GATK-GenomicsDB
DRAGEN GenomicsDB
updated 5 days ago by ▴ 310 • written 5 days ago by • 0
0
votes
0
replies
110
views
Linking AMR Genes to Taxonomy in Soil Metagenomics
metagenomics bacteria wgs AMR resistome
updated 5 days ago by 142k • written 5 days ago by • 0
0
votes
4
replies
249
views
Where to find old version of GATK best practice
gatk
5 days ago by Zhenyu Zhang ★ 1.2k
0
votes
2
replies
214
views
Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis of Spleen Samples from Different Conditions
Seurat scRNA-Seq Single-Cell
5 days ago by Shukai • 0
0
votes
0
replies
141
views
Job: PhD position for metagenomics analysis at the University of Udine
metagenomics
updated 5 days ago by 44k • written 5 days ago by ★ 3.0k
0
votes
3
replies
180
views
Generating a Bed file from a Fasta file
bed NullSeq
updated 5 days ago by 44k • written 5 days ago by • 0
0
votes
3
replies
1.8k
views
Running STRUCTURE from command line
STRUCTURE
updated 5 days ago by 44k • written 3.0 years ago by ▴ 10
0
votes
0
replies
97
views
News: Online course- Advanced Python for Life Sciences
Python-Programming Data-Visualisation Machine-Learning
updated 5 days ago by 44k • written 6 days ago by ★ 2.5k
0
votes
3
replies
193
views
Where are the illumina adapters on Trimmomatic take from?
rna-seq trimmomatic
updated 5 days ago by 142k • written 5 days ago by ▴ 150
0
votes
4
replies
244
views
Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
GATK UnifiedGenotyper
5 days ago by shpak.max ▴ 50
0
votes
1
reply
185
views
Multi-ploid data in ANGSD and NGSadmix
ancestry diploid haploid admixture
updated 5 days ago by ▴ 20 • written 6 days ago by • 0
0
votes
2
replies
432
views
transanno liftvcf "Error: length of chromosome [chr] is not equal to length in chain file. Are you using correct reference?"
liftover transanno
5 days ago by ezz3 • 0
0
votes
0
replies
104
views
Kegg Pathways to Circos
Genomics KEGG Circos
5 days ago by dlera.lozano ▴ 10
0
votes
4
replies
342
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart ensembl wheat python pybiomart
5 days ago by Luqman • 0
0
votes
3
replies
251
views
z-score of gene set
z-score scRNA gene-set
5 days ago by Hien • 0
0
votes
2
replies
195
views
vcf phasing
beagle WhatsHap phasing
5 days ago by safeassli ▴ 10
0
votes
1
reply
156
views
Mapping difference with BWA
variant-calling samtools bam BWA genomics
updated 5 days ago by 82k • written 5 days ago by • 0
0
votes
0
replies
90
views
Rescaling normalized enrichment score (NES)
heatmap
5 days ago by CTLong ▴ 110
0
votes
3
replies
305
views
Kraken2 Custom Database non-deterministic results
Metagenomics kraken2
updated 5 days ago by 6.4k • written 6 days ago by • 0
0
votes
0
replies
119
views
DIFFBIND boxplot results, p value not significant
DiffBind ChIP-seq
4 days ago by RD ▴ 10
0
votes
1
reply
154
views
How to get 2 seurat objects into a DEseq
Seurat DEseq
updated 4 days ago by 44k • written 5 days ago by • 0
0
votes
0
replies
105
views
How to find nucleotide changes and the predicted effect when comparing two genomes
BLAST alignment
updated 4 days ago by 44k • written 4 days ago by • 0
0
votes
0
replies
103
views
KEGG pathway enrichment analysis in Zea mays with R
KEGG Zea-mays R
updated 4 days ago by 44k • written 4 days ago by • 0
0
votes
0
replies
103
views
News: Bioinformatic Analysis of Transposable Elements course
Genome-Annotation TE Manual-Curation Transposable-Elements
updated 4 days ago by 44k • written 4 days ago by ★ 2.5k
0
votes
1
reply
133
views
No output when converting transcript IDs to gene symbols
RNA-seq
updated 4 days ago by 44k • written 4 days ago by ▴ 160
0
votes
0
replies
110
views
MAFFT alignment report
RNA Alignment MAFFT Linux
updated 4 days ago by 44k • written 5 days ago by • 0
0
votes
1
reply
145
views
Small secondary peak for per sequence GC content - FASTQC results (bulk RNA-seq)
RNAseq
updated 4 days ago by 142k • written 4 days ago by • 0
0
votes
0
replies
96
views
Cancer vs Normal Cell Classification Based on SNVs
cancer
4 days ago by dglad • 0
0
votes
4
replies
225
views
merge overlaps and remove non overlap genomic windows
BED intersection overlap
4 days ago by reza ▴ 300
0
votes
6
replies
287
views
from CRAM to fastq
FASTQ WGS CRAM
updated 4 days ago by 82k • written 4 days ago by • 0
0
votes
0
replies
93
views
Phyloseq returning black bars for plot_bar
phyloseq bioconductor R
4 days ago by Jacob • 0
0
votes
0
replies
92
views
miloR - object 'as.SimpleList' of mode 'function' was not found when running calcNhoodDistance
scRNA-seq seurat miloR
4 days ago by shuaizh117 ▴ 10
0
votes
0
replies
101
views
Extracting haplotype-specific annotations from splicing graph
vg
4 days ago by Juhyun • 0
0
votes
0
replies
118
views
Subset of ATAC-seq peaks has high variance
atac-seq edgeR R normalization
4 days ago by Tim • 0
182 results • Page 3 of 4
Recent Votes
Answer: Error with BiocParallel. No barcodes files found
Error with BiocParallel. No barcodes files found
Comment: How do we do quantification using stringtie merge option for all the merged samp
Answer: bcftools view error: the tag "mis" is not defined in the VCF header
Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
Search within posts based on tags using the Biostars API
Extract ENSEMBL IDs from processed Seurat object instead of gene symbols
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Recent Replies
Comment: How do we do quantification using stringtie merge option for all the merged samp by Varsha • 0
Thank you for the detailed explanation.
Answer: How can run cd-hit-est with a clstr threshold less than 0.8? by Asaf 10k
For future reference The 0.8 identity threshold for EST (nucleotides) is hardcoded. However, there's an option to use `-D` (distance) in…
Answer: Tools for chromosomal aneuploidy detection by a.alnawfal.1992 ▴ 260
As far as I know, all the tools utilised control group to compute the z score for chromosomal aneuploidy. but is your goal detect chromosom…
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by Sara ▴ 30
I used Seurat, and in Seurat, I have gene names (which some are with gene-symbols and some with ENSG ids). Then I did Pseudobulk. how can …
Comment: How to decrease the motif score? by ATpoint 82k
So you scan the entire genome and got nothing significant? Is that the issue?
Comment: perl Error - needLargeMem Bigwig by b.contreras.moreira ▴ 200
A quick search suggests the problem is your empty input file? See <https://biostar.galaxyproject.org/p/6794>
Comment: Invalid CIGAR after using bam clipOverlap by MboiTui ▴ 20
ooh good pickup. Might not be the problem but definitely not helping. Will re-run with streamlined workflow and with double quotes and see …
Comment: Invalid CIGAR after using bam clipOverlap by Pierre Lindenbaum 162k
may be not the problem but why this ` RG:Z:H7J22DRX3.${lane}-1C23074F ` in the RG. you're using single quotes with bwa-mem and it won't …
Comment: Invalid CIGAR after using bam clipOverlap by MboiTui ▴ 20
Hello Pierre, Thanks for your reply and insight. with samtools view | grep using the erroneous CIGAR string I get: A00152:841:H7J22D…
Comment: Invalid CIGAR after using bam clipOverlap by Pierre Lindenbaum 162k
please, show us the following output: samtools view "${Ind1}_sorted_dup.bam" | grep -F "A00152:841:H7J22DRX3:2:1112:5267:11397" Furth…
Comment: Failed to download data from EBI with ascp by 孝中 • 0
Hi, have you found the solution to this problem?
Comment: samtools write-index by R.L. • 0
Oh God, thank you so much for helping me in both platforms! I am gonna upgrade my samtools to stay tracked with you and your team! Thank yo…
Answer: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by jared.andrews07 ★ 17k
Go back to your original counts matrix or input data and assign consistent IDs during its generation.
Answer: Facing problem with single cell rna seq annotation using singleR by jared.andrews07 ★ 17k
A few things. >(1)What did i do wrong here? SingleR will annotate each cell with whatever it's most similar to in the reference datas…
Comment: Harmony integration group.by.var parameter by jared.andrews07 ★ 17k
Couldn't tell you, I avoid Seurat like the plague.
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