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699 results • Page 2 of 14
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0
votes
0
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89
views
Last step of metagenome analysis before visualization
metagenome python analyis
1 day ago by Ayda Ecem • 0
0
votes
3
replies
158
views
Generating a Bed file from a Fasta file
bed NullSeq
updated 1 day ago by 44k • written 1 day ago by • 0
0
votes
3
replies
1.8k
views
Running STRUCTURE from command line
STRUCTURE
updated 1 day ago by 44k • written 3.0 years ago by ▴ 10
1
vote
3
replies
555
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics bootstrap
updated 1 day ago by ▴ 160 • written 5 weeks ago by ▴ 40
0
votes
0
replies
88
views
Calculated LAI is too large
annotation LAI assembly TE genome
1 day ago by Yao ▴ 30
1
vote
1
reply
735
views
Herald: The Biostar Herald for Monday, November 01, 2021
herald
written 2.6 years ago by 2.8k
19
votes
10
replies
7.3k
views
7 follow
T2T-CHM13 "complete" human genome gff/gtf annotation file
genomics
written 3.0 years ago by ▴ 590
0
votes
0
replies
88
views
How to recover the entire sequence from all_contig_annotations.csv?
VDJ single-cell TCR-seq cellranger 10x
1 day ago by dawnyipingzou • 0
0
votes
4
replies
226
views
Where to find old version of GATK best practice
gatk
1 day ago by Zhenyu Zhang ★ 1.2k
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
0
votes
0
replies
90
views
News: Online course- Advanced Python for Life Sciences
Python-Programming Data-Visualisation Machine-Learning
updated 1 day ago by 44k • written 1 day ago by ★ 2.5k
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
2
replies
206
views
Elbow plot question (scRNA seq data analysis - scanpy tutorial)
scanpy
2 days ago by ojaswinipandey • 0
1
vote
4
replies
296
views
How to find SRA sequences of some fungal whole genome sequences if only Biosample ID is available?
SRA whole-genome-sequencing NCBI
updated 2 days ago by 44k • written 2 days ago by • 0
2
votes
4
replies
238
views
Filter Genome for Specific Sites
bedtools
updated 2 days ago by 44k • written 2 days ago by • 0
0
votes
3
replies
250
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 2 days ago by ▴ 130 • written 2 days ago by ▴ 20
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
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
2
votes
0
replies
132
views
Herald: The Biostar Herald for Monday, May 20, 2024
herald
2 days ago by Biostar 2.8k
3
votes
5
replies
435
views
Super ehancers
enhancers
updated 1 day ago by ★ 17k • written 20 days ago by • 0
0
votes
2
replies
181
views
vcf phasing
beagle WhatsHap phasing
17 hours ago by safeassli ▴ 10
0
votes
2
replies
206
views
How to generate an Upset plot in R to plot the shared variants between cell free DNA samples
r Upset
2 days ago by sainavyav22 • 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
2
replies
191
views
How to find identical sequences in genome fasta file (by Python or any possible program) ?
fasta
updated 2 days ago by 44k • written 2 days ago by ▴ 10
0
votes
3
replies
200
views
GATK Structural Variants Pipeline - Steps
SV GATK Variant-Calling
updated 2 days ago by 44k • written 2 days ago by ▴ 20
0
votes
0
replies
93
views
Is it possible to keep gene_id and gene_name columns using Seurat::Read10X?
Seurat single-cell scRNA-seq
updated 2 days ago by 44k • written 2 days ago by ▴ 20
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
0
replies
83
views
ENCORI or starBase : ceRNA data retrieval using Web API and curl
ceRNA ENCORI curl microRNA starBase
2 days ago by V_Vibes • 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
101
views
transcriptome annotation
annotation trinity transcriptome
updated 2 days ago by 44k • written 2 days ago by • 0
0
votes
5
replies
227
views
Why most genes have high padj values
RNA-seq DEG
updated 2 days ago by 44k • written 2 days ago by • 0
7
votes
14
replies
2.9k
views
6 follow
How to find tandem duplications pattern in a DNA sequence
Repeat
updated 2 days ago by ▴ 30 • written 3.1 years ago by • 0
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
0
votes
4
replies
250
views
GO analysis: p-value range
GO R
updated 2 days ago by 4.6k • written 3 days ago by ▴ 20
1
vote
2
replies
231
views
News: ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
BestTalk PlatformPresentation offtopic
updated 1 day ago by 6.4k • written 3 days ago by • 0
0
votes
3
replies
241
views
seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from input file
subseq seqtk extractionproblem
updated 2 days ago by 142k • written 3 days ago by • 0
0
votes
0
replies
103
views
Challenges of Affymetrix probe IDs for grouping similar genes to calculate their mean
R Mean Affymetrix Probes Grouping
3 days ago by Maryam • 0
0
votes
4
replies
339
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
3 days ago by Bibi • 0
1
vote
2
replies
356
views
is there a tool to recover corrupted fastq files
fastq short-read
updated 3 days ago by • 0 • written 3 months ago by ▴ 60
0
votes
0
replies
113
views
handling bio replicates for chromHMM
replicates chromHMM
3 days ago by Hasan_Daaboul • 0
0
votes
0
replies
104
views
Tool for within-sample ligand-receptor analysis (bulk RNA-seq) ?
cell-cell communication ligand-receptor self-regulation
3 days ago by DGTool ▴ 20
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
2
replies
326
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix RNA-Seq Limma DESeq2 edgeR
3 days ago by Ezequiel • 0
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
120
views
problems in installing rDock
rDock
updated 2 days ago by 44k • written 3 days ago by • 0
1
vote
6
replies
1.5k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq cellranger
updated 3 days ago by ▴ 30 • written 8 months ago by ▴ 870
1
vote
2
replies
729
views
Checking chromosome builds for genotyping data
GWAS Liftover PLINK
updated 3 days ago by • 0 • written 2.6 years ago by • 0
1
vote
2
replies
384
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx cibersort error RNA-Seq deconvolution
updated 1 day ago by • 0 • written 3 months ago by ▴ 10
0
votes
0
replies
139
views
Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
R
updated 4 days ago by 162k • written 4 days ago by ▴ 20
699 results • Page 2 of 14
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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