... | ... | @@ -482,6 +482,32 @@ Attention : |
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`kaiju2table -t nodes.dmp -n names.dmp -r phylum -o SampleWithoutHuman_kaiju_MEM_verbose_summary_order.tsv SampleWithoutHuman_kaiju_MEM_verbose.out`
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## Kaiju MEM: merge resume files
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In order to create a table with species names in the first column and in next columns the name of the sample, the percentage of reads assigned to this species in this sample, the number of reads and the taxon id (and the same columns in the same order for others samples), you can join the resume files:
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# Remove header
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```
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sed '1d' Sample1WithoutHuman_kaiju_MEM_verbose_summary_species.tsv > Sample1WithoutHuman_kaiju_MEM_verbose_summary_species_noheader.csv
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sed '1d' Sample2WithoutHuman_kaiju_MEM_verbose_summary_species.tsv > Sample2WithoutHuman_kaiju_MEM_verbose_summary_species_noheader.csv
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sed '1d' Sample3WithoutHuman_kaiju_MEM_verbose_summary_species.tsv > Sample3WithoutHuman_kaiju_MEM_verbose_summary_species_noheader.csv
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...
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```
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# Sort (5th column: species names)
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```
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sort -t $'\t' -k 5,5 Sample1WithoutHuman_kaiju_MEM_verbose_summary_species_noheader.csv > Sample1WithoutHuman_kaiju_MEM_verbose_summary_species_noheader.csv.sort
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sort -t $'\t' -k 5,5 Sample2WithoutHuman_kaiju_MEM_verbose_summary_species_noheader.csv > Sample2WithoutHuman_kaiju_MEM_verbose_summary_species_noheader.csv.sort
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sort -t $'\t' -k 5,5 Sample3WithoutHuman_kaiju_MEM_verbose_summary_species_noheader.csv > Sample3WithoutHuman_kaiju_MEM_verbose_summary_species_noheader.csv.sort
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```
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# Join of 3 tables (3 samples)
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```
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join -t $'\t' -a 1 -a 2 -1 5 -2 5 -e 0 -o auto Sample1WithoutHuman_kaiju_MEM_verbose_summary_species_noheader.csv.sort Sample2WithoutHuman_kaiju_MEM_verbose_summary_species_noheader.csv.sort > kaiju_join_Sample1_Sample2.txt
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sort -t $'\t' -k 1,1 kaiju_join_Sample1_Sample2.txt > kaiju_join_Sample1_Sample2.txt.sort
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join -t $'\t' -a 1 -a 2 -1 1 -2 5 -e 0 -o auto kaiju_join_Sample1_Sample2.txt Sample3WithoutHuman_kaiju_MEM_verbose_summary_species_noheader.csv.sort > kaiju_join_Sample1_Sample2_Sample3.txt
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```
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## Kaiju MEM : merge avec fichiers kraken
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### Sort fichiers kaiju
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