[Genome] Question about Other Refseq tracks - parameters used for blat alignment generation

[Ann Loraine]

Hello,

I have a question about how you generate the "Other RefSeq" tracks.

What parameters do you provide to blat in creating these tracks?

I read this description in the Methods section:

"The RNAs were aligned against the [species] genome using blat; those with
an alignment of less than 15% were discarded. When a single RNA aligned in
multiple places, the alignment having the highest base identity was
identified. Only alignments having a base identity level within 0.5% of the
best and at least 25% base identity with the genomic sequence were kept."

This describes the how the post-alignment filtering works but doesn't
provide the parameters used for the initial blat run.

What parameters do you supply to blat in order to create the initial
alignments?

Sincerely,

Ann Loraine

--
Ann Loraine
Associate Professor
Dept. of Bioinformatics and Genomics, UNCC
North Carolina Research Campus
600 Laureate Way
Kannapolis, NC 28081
704-250-5750
www.transvar.org

[Mary Goldman]

Hi Ann,

One of our developers writes: "Xeno RefSeqs are aligned using
protein-translated BLAT, which is able to align farther evolutionary
distances that DNA BLAT. It also uses repeat masking, which is not done
for the native RefSeq alignments.

The blat parameters are

blat -noHead -repeats=lower -q=rnax -t=dnax -mask=lower"

I hope this information is helpful. Please feel free to contact the mail
list again if you require further assistance.

Best,
Mary
------------------
Mary Goldman
UCSC Bioinformatics Group