[Genome] how to replicate human mRNA tracks

[Pufeng Du]

Hi, 

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I have downloaded the mrna sequence and the genome sequences from UCSC, I
also have the program blat and the pslCDNAfilter on my local machine.

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I tried to replicate the mrna track of human on chrY by using the following
steps. 

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blat chrY.2bit chrY.fa ¨Cq=rna ¨Ct=dna ¨Cfine ¨Crepeats=lower chrY.local.psl

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faPolyASizes chrY.fa chrY.polya

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pslCDnaFilter -minId=0.96 -minCover=0.25 -localNearBest=0.001 -minQSize=20
-minNonRepSize=16 -ignoreNs -bestOverlap -polyASizes=chrY..polya
chrY..local.psl chrY.filter.psl

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where chrY.fa contain all the mRNA sequence which is contained by the
chrY.psl downloaded from Table browser. chrY.2bit is generated from the
chromosome file by faToTwobit

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The chrY.filter.psl is about two times in size of the chrY.psl downloaded
from Table browser. Is there any more filtering steps to create the psl file
which can be downloaded from Table Browser?

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Pufeng Du

---

Pufeng Du, Phd. Candidate
Bioinformatics Division
Tsinghua National Laboratory of Informatics Science Technology 
Department of Automation
Tsinghua University
Beijing 100084, China
Tel: (86-10)62794294#813 (Office)

Email: HYPERLINK
"mailto:dpf05 at mails.tsinghua.edu.cn"dpf05 at mails.tsinghua.edu.cn

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