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699 results • Page 2 of 14
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4
votes
5
replies
473
views
Figures are disappeared from html report of SnpEff
HTML SnpEff
23 days ago by analyst ▴ 50
4
votes
7
replies
633
views
To get p-values for the TPM
P-value TPM RSEM
updated 27 days ago by ★ 6.0k • written 28 days ago by • 0
4
votes
1
reply
347
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 7 days ago by 14k • written 8 days ago by ▴ 30
4
votes
3
replies
3.0k
views
How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when run SamToFastq
samtofasq picard validatesamfile
updated 13 days ago by 162k • written 13 days ago by ★ 1.2k
4
votes
12
replies
4.9k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation Experience Illumina Mouse
updated 13 days ago by ▴ 180 • written 3.0 years ago by ▴ 20
4
votes
2
replies
279
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 18 days ago by 44k • written 19 days ago by ▴ 40
4
votes
1
reply
363
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma voom R
23 days ago by pairedttest ▴ 10
4
votes
9
replies
2.2k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing bowtie2 alignment samtools ngs
updated 19 days ago by • 0 • written 2.2 years ago by • 0
4
votes
1
reply
220
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
8 days ago by J. ▴ 40
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient molecule at bam DNA RG ends clipping damage
updated 14 days ago by ▴ 10 • written 2.6 years ago by • 0
4
votes
0
replies
169
views
Herald: The Biostar Herald for Monday, April 29, 2024
herald
23 days ago by Biostar 2.8k
4
votes
4
replies
3.0k
views
CNVkit for somatic copy number detection
cnv cnvkit exome WES
updated 8 days ago by ▴ 10 • written 5.1 years ago by • 0
4
votes
3
replies
399
views
Kraken2 database
kraken microbialdb database krakendb kraken2
updated 9 days ago by ▴ 150 • written 11 days ago by ▴ 10
4
votes
1
reply
273
views
LD-prune variants while maintaining a list of SNPs
snp vcf plink filtering independent
updated 16 days ago by 11k • written 18 days ago by ▴ 570
4
votes
15
replies
1.7k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR DESeq Differential-Expression RNA-Seq
updated 18 days ago by ★ 7.2k • written 5 months ago by ▴ 10
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq RNA-Seq exon
updated 16 days ago by ▴ 30 • written 6.7 years ago by ★ 1.2k
4
votes
2
replies
203
views
Duplicated sequence samtools
bowtie2 samtools
updated 9 days ago by 142k • written 9 days ago by • 0
4
votes
9
replies
524
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch alignment
5 days ago by Gabriel R. ★ 2.9k
4
votes
7
replies
451
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
9 days ago by Chen • 0
4
votes
5
replies
4.4k
views
Tool: GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly Structural-Variation Variant-Calling
updated 6 days ago by ▴ 520 • written 7.2 years ago by ★ 2.9k
4
votes
5
replies
3.5k
views
How to compare compare two Sam files to check mapping
alignment
updated 14 days ago by ▴ 90 • written 6.4 years ago by ▴ 60
4
votes
6
replies
824
views
7 follow
Heatmap and rna-seq
RNA-Seq Heatmap
updated 25 days ago by ★ 6.0k • written 29 days ago by ▴ 10
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference 38build impute imputation
23 days ago by anna ▴ 20
4
votes
3
replies
451
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc conda nextflow
updated 25 days ago by 3.2k • written 26 days ago by ▴ 40
4
votes
9
replies
646
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA R VARIANCE
updated 1 day ago by ▴ 130 • written 7 days ago by ▴ 20
4
votes
2
replies
291
views
GRCh38.gmap file
gnomix gmap
18 days ago by lorena9132 ▴ 10
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome sequencing singleton SNP filter
updated 22 days ago by ▴ 20 • written 9.7 years ago by ▴ 40
3
votes
0
replies
162
views
News: Interested in Spatial Omics?
Bioconductor Spatial-Omics Spatial-Transcriptomics
updated 29 days ago by 44k • written 29 days ago by ★ 2.5k
3
votes
4
replies
356
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq patch freeze genome
updated 5 days ago by 22k • written 6 days ago by • 0
3
votes
5
replies
463
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome PHG graph
1 day ago by beantkapoor16 ▴ 10
3
votes
2
replies
213
views
Publish a Letter in higher impact vs Research article in lower impact
Article Letter Journal
updated 9 days ago by 82k • written 9 days ago by • 0
3
votes
7
replies
438
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc cutadapt illumina tile paired-end
23 days ago by Sergio A.S. • 0
3
votes
8
replies
646
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
16 days ago by Qroid ▴ 40
3
votes
6
replies
298
views
Problem in getting geo file through GEOQUERY
geoquery Geo
updated 4 hours ago by 44k • written 1 day ago by ▴ 120
3
votes
4
replies
359
views
Truncated metadata file report from ENA Portal API
ena python
12 days ago by Giulia • 0
3
votes
1
reply
232
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair samtools alignment
updated 9 days ago by ▴ 300 • written 13 days ago by ▴ 40
3
votes
3
replies
2.5k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 27 days ago by • 0 • written 22 months ago by ▴ 180
3
votes
8
replies
744
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core 16S amplicon dada2 ampliseq
updated 16 days ago by ▴ 410 • written 20 days ago by ▴ 100
3
votes
5
replies
435
views
Super ehancers
enhancers
updated 1 day ago by ★ 17k • written 20 days ago by • 0
3
votes
2
replies
390
views
what is the purpose of indexing the reference genome (Kallisto)
indexing Kallisto
updated 26 days ago by ★ 6.0k • written 26 days ago by ▴ 10
3
votes
6
replies
541
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 10 days ago by ▴ 20 • written 17 days ago by • 0
3
votes
5
replies
362
views
Generating mpileup file using samtools
mpileup samtools
updated 19 days ago by 21k • written 19 days 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
3
votes
2
replies
190
views
converting transcript IDs (Ensembl) to gene symbols in R
RNA-seq
updated 12 hours ago by 142k • written 1 day ago by ▴ 160
3
votes
0
replies
109
views
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
liftOver ATAC-seq csaw
updated 1 day ago by 44k • written 1 day ago by ★ 1.2k
3
votes
2
replies
436
views
Extract protein sequence
fasta alignment blast
22 days ago by anna ▴ 20
3
votes
6
replies
2.1k
views
7 follow
DNA methylation preprocessing
SWAN DNA methylation Funnorm
updated 26 days ago by 44k • written 2.4 years ago by ▴ 10
3
votes
4
replies
499
views
Design matrix Differential expression analysis
RNA-seq Differential-expression
updated 16 days ago by ★ 7.2k • written 19 days ago by ▴ 40
3
votes
3
replies
303
views
Gene Specific coverage from WGS data
WGS SARS-CoV2
updated 9 days ago by 44k • written 22 days ago by • 0
3
votes
4
replies
431
views
Why gatk VariantAnnotator required bam and coverage files
gatk VariantAnnotator
27 days ago by QX • 0
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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