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Confusion of output #11

Closed Edison2021 closed 5 years ago

Edison2021 commented 5 years ago

Hi The manual ( https://ncbi.github.io/magicblast/doc/output.html) mentions that the 12th column is not used in the output. However, i found a value at this position.

cds 0 100 0 0 0 1 357 1 512 0 99 357 plus plus 357 64^75^160^80^133 1 - 1:0 - - - - 357

Could you help explain what do 12th and 13th columns mean?

Edison

boratyng commented 5 years ago

Hi Edison, The 13th column is used, it is alignment score. Columns 11th and 12th are not used. These are always zero and 99.

The unused columns are meant for the first 12 columns to look like tabular output from blastn, so that a few Magic-BLAST alignments can be piped into Splign (https://www.ncbi.nlm.nih.gov/sutils/splign/splign.cgi), which can compute more accurate alignments. Unfortunately due to changes in splign this functionality no longer works seamlessly and Splign can only handle a few alignments.

Also, we cannot remove the unused columns, because that would change location of other columns and break users' pipelines. We are working on a better tabular format for Magic-BLAST where one would be able to select columns and their order.

Edison2021 commented 5 years ago

Thanks! Grzegorz!