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medvedevgroup / SibeliaZ

A fast whole-genome aligner based on de Bruijn graphs
http://medvedevgroup.com/
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How can I create UCSC a bigMaf track from sibeliaz .maf? #25

Open motutaj opened 3 years ago

motutaj commented 3 years ago

Following steps from UCSC http://200.144.254.2:8001/goldenpath/help/bigMaf.html I cannot create bigMaf.txt

mafToBigMaf genome1 examples/sibeliaz_out/alignment.maf stdout | sort -k1,1 -k2,2n > genome1bigMaf.txt reference databases (genome1) must be first component of every block on line 20

I would appreciate any suggestion

iminkin commented 3 years ago

Hi @motutaj , it seems that the postprocessing program you are trying to run needs every block to contain the reference genome. SibeliaZ does not rely on a reference, so you can probably circumvent this problem by writing a small script that filters out all alignment blocks that do not contain some reference sequence.

dongyangzheng commented 3 years ago

Following steps from UCSC http://200.144.254.2:8001/goldenpath/help/bigMaf.html I cannot create bigMaf.txt

mafToBigMaf genome1 examples/sibeliaz_out/alignment.maf stdout | sort -k1,1 -k2,2n > genome1bigMaf.txt reference databases (genome1) must be first component of every block on line 20

I would appreciate any suggestion

hi ，do you solved these？