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Questions tagged [hts]

High-throughput sequencing.

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Is 16S sequencing cheaper than whole-genome sequencing for taxonomic assignment?

This is adapted from a question posted on reddit In my work, I occasionally get asked about metagenomic sequencing, which (after further questioning) I discover means that the person wants to work out ...
2 votes
1 answer

Targeted hybrid capture bam files showing reads outside target regions in my bed file

Sorry if this is a stupid question I am new to analysing targeted hybrid capture data. I am analysing my HTS data from a targeted hybrid capture enrichment method and subsequent sequencing on a ...
2 votes
1 answer

How to input data for DESeq2 from individual HTSeq count?

I am comparing the gene expression of 2 bacteria under 1 condition. I have now the count tables for 3 tech. replicates for each bacteria. ...
3 votes
1 answer

Detecting broad peaks in sRNA-seq data

What kind of tool would be appropriate do detect "broad peaks" in small RNA-seq sequencing data? MACS2 appears to be developed for ChIP-seq data, but I see that there is a ...
7 votes
3 answers

What is the difference between NGS, 2GS, SBS and HTS?

I've come across a bit of confusion about the initialism NGS, so think it would be a good idea to clarify this term (and similar terms like 2GS, SBS, and HTS) for this site with a bit of discussion. ...
4 votes
2 answers

well identifiers in a 1536-well mtp plate

There's a commonly accepted convention for naming the wells in a 384-well-plate: A01..A24 B01..B24 .. P01..P24 It's concise and unambiguous and thus very useful....
6 votes
1 answer

What is this 5-column sequencing format from 2009?

There is high throughput sequencing data here, and I don't know what format it is in. It was submitted in 2009, and the description says the following: Library strategy: ncRNA-Seq Library source:...
7 votes
1 answer

What unit do I get on the y-axis of a metagene profile plot?

I start with a sorted and indexed bam file ("mapped.bam") representing the mapping of small reads on a reference genome, and a bed file ("genes.bed") containing the coordinates of a set of features of ...