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7 votes
Accepted

What is this 5-column sequencing format from 2009?

This is an early Solexa/Illumina sequencer format. The columns are the identifier to location on the flowcell. I believe the "." was the original placeholder for an unread base, which has ...
Bioathlete's user avatar
  • 2,574
5 votes

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

I am not sure how appropriate it is at this point to still refer to sequencing as next-generation sequencing. The leading NGS technology is Illumina/Solexa that has been around for over 10 years at ...
burger's user avatar
  • 2,199
5 votes

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

Here are my attempts at definitions: Sanger: A method of sequencing that depends on chain-terminatiing dideoxynucleotides. This sequencing uses the differential flow of DNA sequences of different ...
4 votes
Accepted

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

Feel free to @ me in deepTools questions, since I'm the primary developer. For a given bin, the count assigned to it is the number of reads overlapping it, regardless of whether they overlap by 1 or ...
Devon Ryan's user avatar
  • 19.6k
3 votes
Accepted

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

It strongly depends on exactly what your protocol is. Note that there are a good number of tools for QCing capture data (here, here). Off-target reads are a standard observation in capture experiments;...
Maximilian Press's user avatar
3 votes

Detecting broad peaks in sRNA-seq data

The sure why any software should be confined to only broad peaks, but there is two packages that should do what I thing you have in mind. Just to clarify, for smallRNAs peak detection is sometimes ...
Sebastian Müller's user avatar
2 votes

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

When comparing anything targeted to whole-genome sequencing for the purposes of assembly, the targeted approach will always be cheaper, because the total length that needs to be assembled is shorter. ...
gringer's user avatar
  • 14.3k
2 votes

How to input data for DESeq2 from individual HTSeq count?

In case still needed, here is a piece of code that I have used for the same purpose (includes a lot of sanity checks). This is highly likely an overkill as each count file would probably have the same ...
haci's user avatar
  • 4,142
2 votes

well identifiers in a 1536-well mtp plate

and here's a scheme I made up myself: AA01..AA48 .. AZ01..AZ48 BA01..BA48 .. BF01..BF48 Pros: alphabetic sorting of well ids does what you expect it's clear ...
user829755's user avatar
2 votes

well identifiers in a 1536-well mtp plate

Here's one way I found: A01..A48 .. Z01..Z48 AA01..AA48 .. AF01..AF48 Pros: Excel does it like that with columns it's clear what's the row and what's the column ...
user829755's user avatar

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