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vrmarcelino / CCMetagen

Microbiome classification pipeline
GNU General Public License v3.0
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Obtaining RPM, fragments, and proportion of mapper reads #21

Closed Tj-Idowu closed 3 years ago

Tj-Idowu commented 3 years ago

I followed the quick start for the running kma and added the -ef flag to get the extended features but the results did not show any columns pertaining to the number of reads.

kma -ipe forward_1.fastq reverse_2.fastq -o output -t_db reference -1t1 -mem_mode -and -apm f -ef

vrmarcelino commented 3 years ago

Hi!

This should generate an additional file (extension .mapstat). Did you get that?

Tj-Idowu commented 3 years ago

Thank you