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<p class="MsoNormal">Dear Dev Team,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am writing you because of a discrepancy between the number of alignment blocks stated on your website and the number of alignment blocks which I can find in the associated files.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">On your website you list the details for the 25 eutherian mammals EPO alignment (<a href="https://www.ensembl.org/info/genome/compara/mlss.html?mlss=1102">https://www.ensembl.org/info/genome/compara/mlss.html?mlss=1102</a>) and state that
there is a total of 329,294 blocks.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">After downloading the entire alignment (838 files) in .maf format from (<a href="ftp://ftp.ensembl.org/pub/release-91/maf/ensembl-compara/multiple_alignments/epo_25_eutherian/">ftp://ftp.ensembl.org/pub/release-91/maf/ensembl-compara/multiple_alignments/epo_25_eutherian/</a>)
I unzipped them and utilized awk to count the number of alignment blocks by counting the number of rows starting with an “a”<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">for file in 25_eutherian_mammals_EPO.* ; do awk '$1=="a"{count++}END{print count}' $file >> alignment_block_counts.txt ; done ;
<o:p></o:p></p>
<p class="MsoNormal">awk '{sum+=$1}END{print sum}' alignment_block_counts.txt ;<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The total number of alignment blocks sums up to 165,214 which is around half of what is mentioned on the website, therefore I am a bit confused what this number consists of?
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best regards,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Christian Gross <o:p></o:p></p>
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