#19 Align Reads

[Colin Hercus]

I have a set of reads from a 454 sequencer that I've
aligned against the HS genome and I'm trying to view
these in GBrowse and to zoom into the base level to see
any differences between the reads and reference genome.
However, I have strange problems when zooming into to
100bp and when viewing alignments using the Aligner
plugin. I expect most of this is my own problems in
setting up the GFF and CONF file however I've tried so
many combinations that I figure I need to ask help.
Problems all relate to segments:realign and Aligner
plugin. I seem to get different and strange results
from both.
First issue is that I've created a match and a HSP
record for each read. They're identical except for the
feature. I expect I can create tracks that can use
Aligner and segments/realign without needing to create
two records per read but every attempt fails.
Second issue is how to show reads that matched the -
strand. If I use something like:
chr22 P559 match 14430942 14431030 148 - . Target
Sequence:D8QTS9R01AU3OH 1 91
then Aligner seems to place insert/deletes in reverse.
If I use :
chr22 P559 match 14430942 14431030 148 . . Target
Sequence:D8QTS9R01AU3OH 91 1
i.e. no strand, reversed co-ordinates then Aligner
seems to work but segments:realign produces strange
results.
I've installed GBRowse 1.65 on Windows XP and have used
memory adapter and MySQL to hold the tracks.
I've attached a GFF file, a .conf file and a sequence
file for the reads. The reference sequenceis Homo
Sapiens Chr22 build 36.
Any help in how to configure these tracks would be
appreciated.
Thanks, Colin

[Colin Hercus]

GFF, FA & conf Files

[Scott Cain]

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user_id=616711

Hi Colin,

Please re-ask (ie, copy and paste) this question to the
GBrowse mailing list (gmod-gbrowse@lists.sourceforege.net),
where there is a rather large readership.

Thanks,
Scott