polyA tails inmediary to transcript sequence

[GoogleCodeExporter]

For which program(s) you want a new feature?
(Capacitor/Simulator/Both/Tetris)
Simulator

Which build of the program(s)?
(look it up in the .prop file in the ./bin folder of the installation)
20100330

What operating system you use?
(unix32, unix64, win32, win64, macPPC32, macX8632, macX8664, other;
see /proc/cpuinfo, Settings->Control Panel->System, Apple->About this Mac)
all

What steps will reproduce the problem?
1. sequencing reads
2.
3.

What is the expected output? What do you see instead?

transcript sequence (expected)

CTACTCGCATGTAGAGATTTCCACTTATGTTTTCTCTACTTTCAGCAACCGAGAAGAGAACCCACGTTTGAACAAGTATC
GGCGTGTGGACAACAGCTAT

obtained reads

>2L:7529-9491W:FBtr0089256:24:1773:25:77:25:77|P1|2L:7552:7605:+
TTATGTTTTCTCTACTTTCAGCAACCGAGAAGAGAACCCACGTTTGAACAAGTaaaaaaaaaaaaaaaaaaaaaa
>2L:7529-9491W:FBtr0089256:24:1773:25:77:25:77|P2|2L:7552:7605:-
ttttttttttttttttttttttACTTGTTCAAACGTGGGTTCTCTTCTCGGTTGCTGAAAGTAGAGAAAACATAA 

Feel free to provide any additional information below.

Original issue reported on code.google.com by gmicha@gmail.com on 20 Apr 2010 at 3:43

[GoogleCodeExporter]

Confirmed, poly-adenylation module appended [a]+ respectively [t]+ to truncated
reads, i.e., reads obtained from fragments shorter than the read 
length-regardless of
their location in the transcript.

Problem incurs especially when no fragment size filtering step (gel 
segregation) is
carried out.

Original comment by gmicha@gmail.com on 20 Apr 2010 at 3:46

• Changed state: Accepted

[GoogleCodeExporter]

Fixed, truncated reads are now truncated, i.e., shorter than the desired read 
length.
Reads that fall partially or entirely in the poly-A tail in contrast get 
appended
[a]+ or [t]+

Truncated reads could be filled up with sequencing primer/ligator sequences, or
directly be omitted. Currently this is left for post-processing steps.

Original comment by gmicha@gmail.com on 20 Apr 2010 at 3:49

• Changed state: Fixed