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178 results • Page 3 of 4
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2
votes
1
reply
262
views
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
updated 4 days ago by ★ 7.2k • written 5 days ago by • 0
0
votes
1
reply
189
views
perseus software (version 1.5.5)
preseus mass spectrometry data
updated 6 days ago by ▴ 20 • written 7 days ago by • 0
0
votes
1
reply
140
views
GO analysis: Indicate genes corresponding to the pathway
GeneOntoloy GO R
updated 2 days ago by ▴ 130 • written 2 days ago by ▴ 20
0
votes
1
reply
106
views
How to hide label in layout file of MCscan (python version)
MCscan
updated 2 days ago by 142k • written 2 days ago by • 0
0
votes
1
reply
607
views
Illumina methylation EPIC V2 array
ewas methylation enrichment missMethyl EPIC
updated 2 days ago by ▴ 40 • written 8 months ago by • 0
1
vote
1
reply
126
views
Generating Group/Cluster Lists from fastq files
Sequencing RNA-seq DNA-Seq
updated 2 days ago by 142k • written 2 days ago by • 0
0
votes
1
reply
465
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 5 days ago by 142k • written 5 days ago by • 0
0
votes
1
reply
92
views
No output when converting transcript IDs to gene symbols
RNA-seq
updated 4 hours ago by 44k • written 13 hours ago by ▴ 160
0
votes
1
reply
114
views
Nextflow docker: Error response from daemon
sarek gatk4 docker nextflow
updated 1 day ago by 162k • written 1 day ago by ▴ 200
1
vote
1
reply
735
views
Herald: The Biostar Herald for Monday, November 01, 2021
herald
written 2.6 years ago by 2.8k
0
votes
1
reply
169
views
Add line under stat test
stats R
updated 5 days ago by ▴ 20 • written 7 days ago by • 0
1
vote
1
reply
211
views
API kegg - IndexError: list index out of range
kegg API
updated 5 days ago by ▴ 20 • written 6 days ago by • 0
0
votes
1
reply
125
views
CreateSeuratObject taking very long
seurat
updated 1 day ago by ★ 1.6k • written 1 day ago by • 0
1
vote
1
reply
209
views
Tool: Collect dispersed executable files and run them by using bingo.
bingo
updated 6 days ago by 44k • written 6 days ago by ▴ 10
0
votes
1
reply
131
views
DRAGEN gVCF files and joint calling GATK-GenomicsDB
DRAGEN GenomicsDB
updated 1 day ago by ▴ 300 • written 1 day ago by • 0
0
votes
1
reply
186
views
What's next after GATK variant calling pipeline?
GATK pipeline figures DNA-seq
updated 6 days ago by 54k • written 7 days ago by ▴ 30
1
vote
1
reply
196
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 6 days ago by ▴ 460 • written 16 days ago by ▴ 10
0
votes
1
reply
66
views
Small secondary peak for per sequence GC content - FASTQC results (bulk RNA-seq)
RNAseq
updated 4 hours ago by 142k • written 4 hours ago by • 0
0
votes
1
reply
45
views
Flag multiple filtering steps on VCF files using VEP
FILTERING VEP VCF
updated 3 hours ago by 162k • written 3 hours ago by ▴ 30
0
votes
1
reply
152
views
Multi-ploid data in ANGSD and NGSadmix
ancestry diploid haploid admixture
updated 1 day ago by ▴ 20 • written 1 day ago by • 0
1
vote
1
reply
227
views
mitochondrial genome assembly pipeline
mammals mitochondrial-genome
updated 6 days ago by 44k • written 6 days ago by ▴ 30
0
votes
1
reply
602
views
scRNAseq quality control weird double curve in nFeature vs nCount plot
scRNA-seq QC single cell BDRhapsody analysis
updated 6 days ago by ▴ 20 • written 13 months ago by • 0
0
votes
1
reply
118
views
Mapping difference with BWA
variant-calling samtools bam BWA genomics
updated 16 hours ago by 82k • written 19 hours ago by • 0
0
votes
1
reply
123
views
How do we do quantification using stringtie merge option for all the merged samples generated.
stringtie quantification
updated 16 hours ago by 82k • written 19 hours ago by • 0
3
votes
1
reply
123
views
vg autoindex seems stuck after a week of running
vg pangenome
updated 14 hours ago by ▴ 380 • written 17 hours ago by ▴ 10
0
votes
1
reply
164
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base calling nanopore simplex dorado duplex
updated 6 days ago by 142k • written 7 days ago by ▴ 10
0
votes
1
reply
172
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat scRNA R
updated 6 days ago by ★ 2.9k • written 7 days ago by ▴ 90
0
votes
1
reply
118
views
How to get 2 seurat objects into a DEseq
Seurat DEseq
updated 4 hours ago by 44k • written 22 hours ago by • 0
1
vote
1
reply
120
views
Construction of circos plot from WGS data
WGS Circos
updated 4 hours ago by 44k • written 12 hours ago by ▴ 10
1
vote
1
reply
211
views
constructing pangenome through psvcp
psvcp pangenome
4 days ago by analyst ▴ 50
0
votes
1
reply
150
views
PCA Visualization error in R - arguments imply differing number of rows
SNPs PCA GBS LINUX r
updated 2 days ago by 11k • written 2 days ago by • 0
1
vote
1
reply
183
views
geom_bar issue in ggplot2 with xlim()
geom_bar ggplot2 statistics R
updated 3 days ago by 82k • written 3 days ago by • 0
0
votes
1
reply
190
views
Broad and Narrow peaks
ATAC ChIP seq
updated 4 days ago by 82k • written 4 days ago by ▴ 20
0
votes
0
replies
165
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG pangenome PHG_v2
6 days ago by Jsarria.EEAD • 0
0
votes
0
replies
60
views
KEGG pathway enrichment analysis in Zea mays with R
KEGG Zea-mays R
updated 4 hours ago by 44k • written 9 hours ago by • 0
0
votes
0
replies
60
views
News: Bioinformatic Analysis of Transposable Elements course
Genome-Annotation TE Manual-Curation Transposable-Elements
updated 4 hours ago by 44k • written 12 hours ago by ★ 2.5k
0
votes
0
replies
120
views
problems in installing rDock
rDock
updated 2 days ago by 44k • written 3 days ago by • 0
0
votes
0
replies
149
views
qPCR gene expression data analysis
qPCR geneexpression anova
6 days ago by ebertomeup • 0
0
votes
0
replies
74
views
Kegg Pathways to Circos
Genomics KEGG Circos
21 hours ago by dlera.lozano ▴ 10
0
votes
0
replies
151
views
How can i use ESM-1v ?
VEP ESM-1v
4 days ago by Meto • 0
0
votes
0
replies
157
views
How to deal with possibly important predictors omitted during the building of an OLS multivariant linear regression model?
multivariant-linear-regression
updated 2 days ago by 44k • written 2 days ago by ▴ 20
0
votes
0
replies
152
views
sci-RNA-seq
cell single seurat sci-rna-seq counts
5 days ago by kilcdincer ▴ 10
0
votes
0
replies
94
views
News: Online course: Network analysis in Systems Biology with R/Bioconductor
Bioconductor Systems-Biology Network-Analysis R
updated 2 days ago by 44k • written 2 days ago by ★ 2.5k
0
votes
0
replies
148
views
Tera-scale metagenomic coassembly tool
co-assembly Metagenomics
4 days ago by Moinuddin • 0
0
votes
0
replies
63
views
Rescaling normalized enrichment score (NES)
heatmap
16 hours ago by CTLong ▴ 110
2
votes
0
replies
190
views
Tool: Sequence alignment on split read event such as inversion, duplication and complex nested events.
minimap alignment NGMLR
3 days ago by micah ▴ 30
0
votes
0
replies
157
views
cat-bgen fail
bgenix
updated 6 days ago by 44k • written 6 days ago by • 0
0
votes
0
replies
154
views
select set of intervals that cover a genomic region
GRanges bed
6 days ago by ntsopoul ▴ 60
0
votes
0
replies
156
views
Understanding behaviour of SCTransform in Seurat
Seurat scRNASeq normalization
updated 5 days ago by 142k • written 5 days ago by ▴ 90
2
votes
0
replies
132
views
Herald: The Biostar Herald for Monday, May 20, 2024
herald
2 days ago by Biostar 2.8k
178 results • Page 3 of 4
Recent Votes
Answer: Microbial community analysis pipelines in metagenomics
A: What are chimeric reads?
Answer: Allele count of 2 for homoplasmic MT variants in VCF
Find count of reads in BAM file that fall within BED region
Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
C: Reads mapped to another chromosome in paired-end data of RNA-seq
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Recent Replies
Comment: Mouse or Rat Gene Expression Data Similar to GTEx by GenoMax 142k
Past thread: https://www.biostars.org/p/178266/
Answer: Mouse or Rat Gene Expression Data Similar to GTEx by GenoMax 142k
Mouse bodymap samples : https://ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA375882%20&o=acc_s%3Aa
Answer: Mouse or Rat Gene Expression Data Similar to GTEx by bk11 ★ 2.5k
Here is the [RatGTEx][1] [1]: https://ratgtex.org
Comment: Random Access remote BAM files by a.penatauber • 0
Hi Lucas, I am looking for a similar functionality as I'm working with a large volume of CRAM files on S3, and downloading them whole would…
Comment: from CRAM to fastq by ATpoint 82k
Yes, but I still think that with this syntax you get an uncompressed file, because samtools does not detect the gz suffix. Just take a `hea…
Comment: merge overlaps and remove non overlap genomic windows by reza ▴ 300
Overlap of "Ch1 200 250" and "Ch1 150 220" is "Ch1 200 220", but I want to combine windows that have overlap. Thus, my goal is to combine …
Comment: Flag multiple filtering steps on VCF files using VEP by Pierre Lindenbaum 162k
I don't understand that question.
Comment: merge overlaps and remove non overlap genomic windows by Pierre Lindenbaum 162k
> But your answer is exactly the opposite of what I want oh I see. but i don't understand the logic why: "Ch1 200 250" and "Ch1 150 220" …
Comment: merge overlaps and remove non overlap genomic windows by reza ▴ 300
sorry i edited my example. But your answer is exactly the opposite of what I want
Answer: merge overlaps and remove non overlap genomic windows by Pierre Lindenbaum 162k
> have two bed files these are not bed files. A chromosome is missing in chromosome 1 > How can I create a file from the two mention…
Comment: Small secondary peak for per sequence GC content - FASTQC results (bulk RNA-seq) by GenoMax 142k
Have you checked for presence of rRNA in the affected samples? That can be one possibility for these peaks. In theory if you are aligning …
Comment: Allele count of 2 for homoplasmic MT variants in VCF by GenoMax 142k
Please accept the answer (green check mark) to provide closure to this thread.
Comment: Trimmomatic running but files containing purged reads are empty by GenoMax 142k
Perhaps there were no low quality reads either.
Comment: Allele count of 2 for homoplasmic MT variants in VCF by Arton ▴ 10
Thank you for the helpful answer!
Comment: How to get the ratio of allele counts from GATK derived VCF file? by DBScan ▴ 300
I think GATK only counts informative reads in AD, do you have a DP field? DP should be closer what FreeBayes reports. You can also check GA…
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