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3
votes
8
replies
1.4k
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 10 months ago by ▴ 420 • written 10 months ago by ▴ 100
1
vote
2
replies
812
views
16S amplicon sequencing input data (spreadsheet): barcode vs. linker primer seqs?
barcode amplicon 16s
15 months ago by sovrappensiero ▴ 100
17
votes
8
replies
2.2k
views
Where do find virulence gene information in a gff/gtf file?
microbial genomics gff annotation gtf
2.0 years ago by sovrappensiero ▴ 100
5
votes
5
replies
1.2k
views
Simulating metatranscriptomic shotgun reads
metatranscriptomic RNA simulated-reads shotgun-sequencing
updated 2.1 years ago by ★ 29k • written 2.1 years ago by ▴ 100
2
votes
3
replies
959
views
biological vs. technical definition of "insert size"
grinder simulated-reads shotgun-sequencing
updated 2.1 years ago by 87k • written 2.1 years ago by ▴ 100
0
votes
4
replies
1.3k
views
Alternative to NCBI nt for MEGAN-LR?
taxonomy database pacbio index smrt
updated 2.9 years ago by ▴ 40 • written 2.9 years ago by ▴ 100
6
votes
7
replies
4.4k
views
kallisto "gene" counts
gtf rna-seq kallisto
updated 2.8 years ago by 45k • written 3.0 years ago by ▴ 100
5
votes
12
replies
4.3k
views
Secrets to finding metadata on SRA data?
metadata sra ncbi biosample bioproject
updated 3.0 years ago by 23k • written 3.1 years ago by ▴ 100
0
votes
0
replies
733
views
NCBI EUtils: identifying projects with both NGS and Sanger sequencing
ncbi eutils data type
4.4 years ago by sovrappensiero ▴ 100
7
votes
11
replies
3.1k
views
Elink to get PMID associated with a BioProject or SRA entry
eutils ncbi bioproject pmid pubmed
updated 4.4 years ago by 102k • written 4.4 years ago by ▴ 100
1
vote
3
replies
1.5k
views
primersearch Illegal character '/' error: EMBOSS An error in primersearch.c at line 499
primersearch emboss error warning
5.3 years ago by sovrappensiero ▴ 100
2
votes
7
replies
2.2k
views
Entrez Direct E-utilities on command line: efilter parameters for limiting efetch results
ncbi efilter efetch elink biosample
updated 5.4 years ago by 150k • written 5.4 years ago by ▴ 100
5
votes
4
replies
11k
views
Normalization scaling factors: formula for applying them to raw counts
normalization edgeR DESeq2 R
6.8 years ago by sovrappensiero ▴ 100
0
votes
8
replies
2.9k
views
Normalization amplicon data using mean depth and coverage
normalization amplicon depth coverage
6.8 years ago by sovrappensiero ▴ 100
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