Problem With Phastcons
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Entering edit mode
7.8 years ago
vasilislenis ▴ 140

Hello everybody, I am trying to identify the conserved sequences between human, mouse and rut. I am using chromosome 22 of human as a reference and I am giving this command to phastCons to test it:

/phastCons --target-coverage 0.25 --expected-length 12 --rho 0.4 --msa-format MAF ~/Multiple/hg19_mm10_rn4.maf ~/Multiple/init.mod > scores.wig

where the init.mod is the tree for non- conservation, but it gives me the following error:

"cannot disregard reference species (chr22) when reading MAF file"

Is there anyone who may had the same problem?

Please, I need your help Thank you in advance.

conservation multiple-alignment • 1.9k views
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Entering edit mode
6.1 years ago
Penny • 0

Does your maf file contains reference species

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