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Extract Di-nucleotide/Tri-Nucleotide substitution frequencies from MSA/VCF file
MSA substitution VCFstats Evolution VCF
updated 22 days ago by 161k • written 22 days ago by ▴ 50
3
votes
1
reply
406
views
Using DADA2 for finding viral sequence variants
RNASeq Amplicon dada2 Variant
updated 6 months ago by 3.2k • written 6 months ago by ▴ 50
0
votes
0
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332
views
Compute Abundance counts for full-length Sequences?
abundance RNASeq Fasta Amplicon
9 months ago by Saran ▴ 50
3
votes
5
replies
1.3k
views
Comparing P-Values & FDR adjusted p-values between RNA-Seq experiments?
Limma EdgeR Voom RNA-Seq RNA
updated 10 months ago by ★ 7.1k • written 10 months ago by ▴ 50
1
vote
3
replies
798
views
Count SNP per read
VCF SNP RNA-Seq MSA
updated 10 months ago by 6.4k • written 10 months ago by ▴ 50
1
vote
1
reply
454
views
Identifying Mutation Frequency Changes in MSAs over time?
Mutation Fasta MSA MutationRate RNA-Seq
updated 11 months ago by 4.2k • written 11 months ago by ▴ 50
1
vote
2
replies
750
views
Flitering Genes in RNA-Seq causes more significant FDR Adjusted P-Val DEGs?
Limma RNA Voom EdgeR RNA-Seq
updated 12 months ago by 82k • written 12 months ago by ▴ 50
0
votes
0
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289
views
Differential Expression Analysis of single cell data with large difference in cell count for groups.
scRNA seurat DEG
14 months ago by Saran ▴ 50
3
votes
2
replies
658
views
Cause of short sequences in Amplicon Sequencing?
Illumina ASV Amplicon DADA2
14 months ago by Saran ▴ 50
1
vote
1
reply
548
views
Visualize variants and percentage of variants from one sample of Amplicon Seq data?
Amplicon PCR RNAseq GATK BWA
updated 15 months ago by ★ 3.8k • written 15 months ago by ▴ 50
2
votes
1
reply
535
views
Find ASVs for Non-Microbial Data
Amplicon ASV PCR BWA VCF
updated 15 months ago by 3.6k • written 15 months ago by ▴ 50
0
votes
0
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269
views
Display fraction of mutations and variants for Amplicon Sequencing sample?
PCR Amplicon VCF BWA
15 months ago by Saran ▴ 50
6
votes
7
replies
1.7k
views
Error in reference fasta file when indexing with samtools
samtools RNA-seq
updated 10 months ago by 43k • written 15 months ago by ▴ 50
0
votes
2
replies
708
views
Is the RNA- sequencing quality too bad for analysis?
fastQC RNA PCR BWA minimap2
updated 16 months ago by 3.9k • written 16 months ago by ▴ 50
0
votes
0
replies
513
views
BWA-MEM : skip orientation FR as there are not enough pairs ?
PCR sequencing BWA illumina
16 months ago by Saran ▴ 50
1
vote
4
replies
844
views
Align PCR-amplified sequences to two amplicons to get statistics of alignment?
PCR Alignment Amplicon
16 months ago by Saran ▴ 50
2
votes
4
replies
957
views
Remove rRNA for RNA-Seq Analysis
rRNA RNA-Seq EdgeR
updated 17 months ago by 142k • written 17 months ago by ▴ 50
3
votes
5
replies
1.3k
views
Multimapped reads in STAR alignment and subread::featureCounts()
Multimap STAR featureCounts alignment Rsubread
17 months ago by Saran ▴ 50
2
votes
1
reply
499
views
Why do all of my PCR reads not map to the reference sequence?
PCR sequencing BWA illumina
updated 18 months ago by 142k • written 18 months ago by ▴ 50
0
votes
3
replies
706
views
What algorithm to use to align sequences of gene to reference gene and analyze variants?
RNASeq 16S CRISPR Sequencing Fastq
updated 18 months ago by 142k • written 18 months ago by ▴ 50
1
vote
2
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1.5k
views
What do Over-represented Sequences mean in FastQC using RNA-Seq?
fastqc RNAseq trimmomatic adapters
updated 19 months ago by 100k • written 19 months ago by ▴ 50
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