Settings for Tailseeker 3

Analysis Level


You can run Tailseeker for different ranges of provided functions. It can be used for essential tail length measurement only (level 1) or for getting the full gene- level statistics (level 3). Higher level will include all result data from lower level, but it takes much more space, time, and external dependencies.


Third-party Base-calling


The standard basecaller of the Illumina sequencer is sometimes fail to produce high quality basecalls for 5′-side read (usually read 1) when long poly(A) tail is attached on its 3′-side. AYB is much stronger at reliable basecalling in this case, gives 10-50% more mappable reads for tags adjacent to poly(A) tails > 100 nt.


GSNAP Alignment


Tailseeker 3 uses STAR as the primary sequence alignment software. Optionally, GSNAP can be used to rescue unmapped sequences by STAR. Tags with long poly(A) tails sometimes suffer from low sequence read quality, and this leads to failure in identification of tags. Usually, GSNAP rescues ~0.5% of total reads and ~10% among long poly(A) tails. However, it lengthens total running time of the pipeline by about 10-fold.

Do you want to use GSNAP together with STAR?




Sequencing Cycles


Specify sequencing cycle ranges in 1-based right-inclusive coordinates. Please note that Illumina HiSeq usually spend one more cycle for the Index read. In those machines, six nucleotides index will take up seven cycles, whose last cycle needs to be skipped.
from length
from length
from length

Data Sources


Data dir. Lane Chemistry
Delete
Delete
Add

Poly(A) Standards


Poly(A) standards are used for quality checks of poly(A) measurements.
Name Index Length
Add

Experimental Samples


Name Index
Add

Reference Genome


Tailseeker 3 supports EMSEMBL-style genome and gene annotations. If you cannot find an appropriate one in your study, you can use analysis level 1, which does not rely on genome or gene annotations.







Generated Settings

Please copy the following configuration and save it as a file named “tailseeker.yaml” in an empty directory. And, run “tseek run -j” there.