Dear UCSCers, I'm trying to reproduce the Scer2 7-way alignment, as in http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/makeDb/doc/sacCer2.txt
. Before running blastz, genomes are usually faToNib-masked for repeats, like in the example based on ciona alignments: http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto In the yeast alignment, this step is missing. Am I right? If so, why? I mean, which should be the criteria to include/skip this step? . Even if *.nib files are not necessary to feed blastz, it seems that they are necessary to carry out the axtChain-chaining step. Is that right? . Although chain.csh is created for the chaining step, I don't see axtChain invoked anywhere in the pipeline. I can only observe that *.chain files are created somehow and then used to feed chainMergeSort. Could you please clarify how is the chaining step performed? Thanks in advance Meritxell Oliva PhD Student Comparative Bioinformatics Group Bioinformatics and Genomics Programme Centre de Regulacio Genomica (CRG) Dr. Aiguader, 88 08003 Barcelona Spain email: [email protected] . _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
