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
