Hello Smitha, The best course of action depends upon what type of data you have. If you have complete RNA sequences you could input these to our BLAT tool (http://genome.ucsc.edu/cgi-bin/hgBlat) and select "psl" as your output type. Note that BLAT isn't really optimized for cross-species alignments.
Once you have the output in psl format you can copy and paste this output directly into the custom track tool here (http://genome.ucsc.edu/cgi-bin/hgCustom). For more information on the PSL format you can read our FAQ here: http://genome.ucsc.edu/FAQ/FAQformat.html#format2 On the other hand, if you have short-read data, then you might be better off using a short-read aligner such as BWA, possibly followed by TopHat/Cufflinks and viewing alignments as a BAM custom track. This process is beyond the scope of this mailing list but there are standard workflows for this and you can find support here as a start: seqanswers.com If you have RNA-seq data for other species mapping short reads to human probably won't work very well. One possibility: You could use a standard RNA-seq mapping flow to the genomes of the other organisms, translate the results to PSL, and then use pslMap (one of the utilities in the the kent source tree) with a .over.chain file to make a PSL for human. You can read more about obtaining and using our source tree here: http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 3/7/12 9:46 AM, Smitha Pulukuri wrote: > Hi > > If I have the FASTA sequence then how can we convert the data to build a > custom track.Please let me know. > > Thanks > Smitha > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
