Dear Suma, It looks like you want fasta files with alignments to contigs. If that is the case, you can try to use pslPretty (a tool available in the source code) to generate AXT format, then you will need to write some Perl or Awk to massage the AXT format into the FASTA format that you want.
Below is a link on how you can download the source which is free for academic, nonprofit, and personal use. A license is required for commercial use. http://genome.cse.ucsc.edu/FAQ/FAQlicense#license3 You can access the source code through our git repository: http://genome.ucsc.edu/admin/git.html or a zip file: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip Please note the build instructions: http://genome.ucsc.edu/admin/jk-install.html All of the kent utilities output their usage message and command line options by running them with no arguments. 1. Use BLAT to get psl output. 2. Use pslPretty on the psl output to generate the axt format. Here is pslPretty's usage and command line options: pslPretty - Convert PSL to human readable output usage: pslPretty in.psl target.lst query.lst pretty.out options: -axt - save in something like Scott Schwartz's axt format Note gaps in both sequences are still allowed in the output which not all axt readers will expect -dot=N Put out a dot every N records -long - Don't abbreviate long inserts -check=fileName - Output alignment checks to filename It's a really good idea if the psl file is sorted by target if it contains multiple targets. Otherwise this will be very very slow. The target and query lists can either be fasta, 2bit or nib files, or a list of fasta, 2bit and/or nib files one per line If you have further questions, please contact the mailing list. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Suma Avasthi" <[email protected]> To: [email protected] Sent: Thursday, March 17, 2011 12:00:07 AM Subject: [Genome] Reg: BLAT Dear Sir/Madam, We have performed BLAT and are stuck up at the point of generating .pslx file, we have got the .pslx file which is supposed to include the sequence with reference to the reference genome position. So, right now we have this file, but our query is how to get these alignments into continuous contigs with respect to the reference genome. Below is the format we are expecting. Please do let us know any suggestions how to get the sequences from the .pslx file into continuous contigs. Kindly let us know any tools or scripts already present with BLAT which we can use.* >NODE_829_length_188_cov_58.063831|NC_000921.1|522104|522311|-* TTCAAACAATCTAGCGCTTGTTGTTTCAATCTTTCTATGGCTTCTTTAGA CAAGCCTTTCAAGCATTCGTTTTTCTCAGCTTCTGTTTTGGCGTTTTTGA TACAATCCTTATACTCTTGAAGCTCTTTTTGAAGCTCTAATTCCTTACGG AATTTCTCTCTAATCTCAGGGTCATTTATGAGTTTTAGGCACTCTTTCCG TTCTTCAT *>NODE_686_length_576_cov_70.845490|NC_000921.1|522324|523357|+* TTTTCAAACAATCTAGAGCCACTTGAACTTTTTGTTGGTTCAGTAAGCTT TTTTTCAGGTTTTCATCTTTGATTAAATCTAAACACTTGATCCTTTCTTC TTCAGTTTTGGCATTTTTGATGCAGTCGTTATAAGCCTCTAGAGTCTTTT TCATTTGATCTTGAAGTTTTTTGTCTTTGATAAGCTTCAAACATTCTTCA TAGTTGCCACCATTACTAATACACTCATAAAAGGCTCTCAATGGGTTTTT GTCCTCAATTTCTGCAATATTCAAATAGTTGTATAAGGTTCTATTGGGAT CGTCATTGAAGAAAAGATTCTTATCGATCATATTGCCTTTTTCATTCCGT TCTTTCAGTAATCGGTTATACTCTTGCCTTATTTGGATTTCATCATTGAC ATAAAGATTCCTGTCTTTGCTAAAACGAGAGCTTTTATCTTCCAAAGGTA CAAAGTAGTGAAAAATGCTTCTAGAAAATAAAATAATCACGATAAGAACA GCGACTACAATGCCGCCAATAATGTATTTCTTTTTGCTTCCTTTGATAAT CTCTTGATCGTTAGAGTCGTCAGTTATTTCTTCTAGCTTGTCTTCA *>NODE_315_length_254_cov_55.972443|NC_000921.1|523084|523357|-* TTGGGGTGAATCTTGTTGGGTTTTTTCAGAAGTTTCATCATCAATCAAGT CCGTTTGAGTTTCTTCTTGATGCTCATTATTTTCTTGATCGTCTTCTTCG TTCAGTTTTTGGGTTTCTTCATCTAAACTCTTTTGCTGAGTGAAAGGTCT TTTATCATCAACTAATTTTCTGGCTTTCTTGAATAACTTGTCTGCTAGAC TGCCATTGCTAGATTCTGAAGTTTCATTACCTCCAGAATCCATTTGAGTT TGGGTTTCTTCTAGCTTGTCTTCA Thanking you Suma _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
