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695 results • Page 2 of 14
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4
votes
1
reply
219
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
8 days ago by J. ▴ 40
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
0
replies
169
views
Herald: The Biostar Herald for Monday, April 29, 2024
herald
23 days ago by Biostar 2.8k
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
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
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 8 days ago by ▴ 150 • written 11 days ago by ▴ 10
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
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
5
replies
4.4k
views
Tool: GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly Structural-Variation Variant-Calling
updated 5 days ago by ▴ 520 • written 7.2 years ago by ★ 2.9k
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
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
1
reply
344
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
7
replies
631
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
2
replies
290
views
GRCh38.gmap file
gnomix gmap
17 days ago by lorena9132 ▴ 10
4
votes
7
replies
451
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
8 days ago by Chen • 0
4
votes
2
replies
293
views
How can I analyze normalized expression data?
DEseq2 RNA-seq
13 days ago by mnx0723 • 0
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
9
replies
523
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch alignment
5 days ago by Gabriel R. ★ 2.9k
4
votes
5
replies
3.4k
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
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
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
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
7
replies
648
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
23 days ago by e.r.zakiev ▴ 210
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
645
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
5
replies
472
views
Figures are disappeared from html report of SnpEff
HTML SnpEff
23 days ago by analyst ▴ 50
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
6
replies
540
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 9 days ago by ▴ 20 • written 17 days ago by • 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
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
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
5
replies
435
views
Super ehancers
enhancers
updated 1 day ago by ★ 17k • written 20 days ago by • 0
3
votes
4
replies
358
views
Truncated metadata file report from ENA Portal API
ena python
12 days ago by Giulia • 0
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 14 days ago by • 0 • written 5.6 years ago by 8.5k
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
302
views
Gene Specific coverage from WGS data
WGS SARS-CoV2
updated 8 days ago by 44k • written 22 days ago by • 0
3
votes
5
replies
460
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome PHG graph
1 day ago by beantkapoor16 ▴ 10
3
votes
1
reply
118
views
vg autoindex seems stuck after a week of running
vg pangenome
updated 11 hours ago by ▴ 380 • written 14 hours ago by ▴ 10
3
votes
8
replies
743
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
2
replies
186
views
converting transcript IDs (Ensembl) to gene symbols in R
RNA-seq
updated 9 hours ago by 142k • written 1 day ago by ▴ 160
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
0
replies
106
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
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
2
replies
435
views
Extract protein sequence
fasta alignment blast
22 days ago by anna ▴ 20
3
votes
3
replies
323
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk vcf liftover
updated 12 days ago by 44k • written 12 days ago by ▴ 260
3
votes
4
replies
499
views
Design matrix Differential expression analysis
RNA-seq Differential-expression
updated 15 days ago by ★ 7.2k • written 18 days ago by ▴ 40
3
votes
9
replies
653
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 28 days ago by 100k • written 4 weeks 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
3
votes
3
replies
254
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm ChIP-seq consensus peaks
updated 6 days ago by 82k • written 7 days ago by • 0
695 results • Page 2 of 14
Recent Votes
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
How to classify cells based on the expression of genes in scRNA-seq
Answer: Using GATK MarkDuplicates for targeted sequencing data
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Recent Replies
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…
Comment: Multiplexing for pooled CRISPR screen sequencing by Tuấn Anh • 0
Thank you GenoMax! So would we just prepare the dual-indexed library and ask the sequencing service to do single-end sequencing?
Answer: Construction of circos plot from WGS data by marco.barr ▴ 130
Hi Anitha, you can take inspiration from here on which data to use and how to set up your WGS circle plot. [https://www.tandfonline.com/…
Comment: Trimmomatic running but files containing purged reads are empty by Wilber0x ▴ 50
Thanks for the advice, it seems like it is likely I have the incorrect adaptor sequences, though I am still surprised that no low quality r…
Answer: Trimmomatic running but files containing purged reads are empty by GenoMax 142k
> Why is trimmomatic not removing any reads? It is not mandatory that your data have extraneous/adapter sequence. If no extraneous sequenc…
Comment: FastQC interpretation - 16S sequencing by GenoMax 142k
Since a specific region is being amplified it is expected that many of the library fragments will have identical sequences. Thus the low nu…
Comment: FastQC interpretation - 16S sequencing by Christopher ▴ 10
@genomax Thank you so much for replying. I was quite unsure about the qualities. One more question. There is no problem within nucleotide d…
Answer: FastQC interpretation - 16S sequencing by GenoMax 142k
> My specific question is about the feasibility of per base sequence content analysis and whether I should be concerned about a particular …
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