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Results tagged with ngs
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user 4885
use for general applications of high-throughput nucleotide sequencing methods that use short-read technology (e.g. Illumina, IonTorrent). For long-read sequencing, use 'long-read', or a more specific tag if applicable (e.g. nanopore, pacbio).
2
votes
Accepted
chipseeker annotation issue
I had a similar case just recently.
The tssRegion argument ChIPseeker is used to define what is considered a promoter, which is frequently the question at hand. However, ChIPseeker will not perform an …
- 886
1
vote
Which format is the most raw format
BCL (binary base call) files are the most raw data that you will likely get. As a matter of fact, the images taken by the machine each cycle are even more raw but it makes no sense to interact with th …
- 886
5
votes
2
answers
584
views
High percentage of poly A sequences in 10X chromium R2 read
I'm currently analyzing two samples of eosinophil cells isolated from mouse lung and the samples are of very different quality.
According to the Cell Ranger summary 56% of the reads can be mapped to t …
- 886
-1
votes
Accepted
High percentage of poly A sequences in 10X chromium R2 read
I actually figured out what was going on some time ago:
The over-represented sequence is the template switching oligo (TSO) that is used for the synthesis of the second strand (the example is for the …
- 886
1
vote
Are sequencing reads written differently when inserts and indexes are sequenced seperately?
The order of sequencing in a dual index flow cell is:
Read 1
Index 1 (I7)
Index 2 (I5)
Read 2
Between each step there is a switch of the primer used (Read1-primer -> Index1-primer (I7) -> Index2-pri …
- 886
6
votes
Accepted
What is the name of this type of figure?
This kind of visualization showing the banding patterns of chromosomes are called "chromosome ideograms".
You can use for example IdeoViz in R to generate them.
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