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178 results • Page 2 of 4
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1
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2
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729
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Checking chromosome builds for genotyping data
GWAS Liftover PLINK
updated 3 days ago by • 0 • written 2.6 years 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
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
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
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
1
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2
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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
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
1
vote
2
replies
206
views
Elbow plot question (scRNA seq data analysis - scanpy tutorial)
scanpy
2 days ago by ojaswinipandey • 0
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
1
vote
1
reply
735
views
Herald: The Biostar Herald for Monday, November 01, 2021
herald
written 2.6 years ago by 2.8k
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
1
vote
6
replies
362
views
What marks a De-Novo Genome assembly as FAILED?
nanopore denovo illumina assembly genome
1 day ago by Umer ▴ 50
1
vote
2
replies
169
views
How can we convert a vcf to fasta, so that I can blast some genes against that whole genome sequences?
blast fasta vcf gene
updated 1 day ago by 44k • written 1 day 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
1
vote
4
replies
308
views
Filtering VCF files based on VAF giving incorrect results
GATK picard VCF bcftools
updated 1 day ago by 44k • written 7 days ago by ▴ 10
1
vote
3
replies
178
views
Question about samtools view flags (paired reads vs. properly paired reads)
samtools
updated 1 day ago by 162k • written 1 day ago by • 0
1
vote
4
replies
270
views
Genotyping sites with N in reference genome
GATK UnifiedGenotyper
1 day ago by shpak.max ▴ 50
1
vote
3
replies
277
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
21 hours ago by Pegasus ▴ 100
1
vote
10
replies
587
views
Add stats to the plot
R
16 hours ago by Ghada • 0
1
vote
3
replies
175
views
downloading chemical database from ChEMBL
ChEMBL PyRMD Virtual-Screening
updated 12 hours ago by 142k • written 1 day ago by • 0
1
vote
3
replies
155
views
Trimmomatic running but files containing purged reads are empty
fastqc fastq trimmomatic
updated 6 hours ago by 142k • written 6 hours ago by ▴ 50
1
vote
2
replies
146
views
Multiplexing for pooled CRISPR screen sequencing
multiplex CRISPR-screen Illumina
5 hours ago by Tuấn Anh • 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
5
replies
182
views
How to get the ratio of allele counts from GATK derived VCF file?
Freebayes GATK SNP VCF
updated 4 hours ago by 44k • written 9 hours ago by ▴ 230
1
vote
8
replies
782
views
Random Access remote BAM files
htslib BAM
updated 2 hours ago by • 0 • written 3 months ago by ▴ 10
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
2
replies
270
views
How to generate table_annovar from VCF input?
vcf annovar
updated 5 days ago by 162k • written 5 days ago by ▴ 70
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
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
4
replies
250
views
GO analysis: p-value range
GO R
updated 2 days ago by 4.6k • written 3 days ago by ▴ 20
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
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
0
votes
3
replies
297
views
Sam file Header problem
Sam Header problem file
updated 5 days ago by 162k • written 6 days ago by • 0
0
votes
0
replies
140
views
How do I quantify the non-coding transcripts that I have generated after using CPAT,PLEK, and BLAST altogether?
transcript Quantify non-coding
5 days ago by Varsha • 0
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
101
views
transcriptome annotation
annotation trinity transcriptome
updated 2 days ago by 44k • written 2 days ago by • 0
0
votes
6
replies
205
views
from CRAM to fastq
FASTQ WGS CRAM
updated 2 hours ago by 82k • written 11 hours ago by • 0
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
0
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9
views
Error when looping over multiple columns in a data frame in R
Statistics R
16 minutes ago by Mohamed Samir ▴ 20
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
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
2
replies
275
views
How can I calculate the OS of each patient?
overall-survival
2 days ago by Pedro • 0
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
0
votes
4
replies
351
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq scRNA-seq
updated 5 days ago by • 0 • written 7 days ago by ▴ 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
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
120
views
problems in installing rDock
rDock
updated 2 days ago by 44k • written 3 days ago by • 0
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
178 results • Page 2 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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