... | ... | @@ -18,12 +18,12 @@ L-->|gffread| M[Contigs : gff transformed to gtf] |
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M-->|bwa index| N[Indexation contig file]
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N-->|bwa mem| O[Aligned reads]
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O-->|Samtools view \nSamtools sort \nSamtools index| P[.bam file]
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P-->|featureCounts| Q[Transcript expression quantification]
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L-->|fasta_extract.pl| R[Transcripts]
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R-->|bwa index| S[Indexation transcript file]
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P-->|featureCounts| Q[Quantification of gene]
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L-->|fasta_extract.pl| R[Gene]
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R-->|bwa index| S[Indexation gene file]
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S-->|bwa mem| T[Aligned reads]
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T-->|Samtools view \nSamtools sort \nSamtools index| U[.bam file]
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U-->|Samtools idxstats| Q[Transcript expression quantification]
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U-->|Samtools idxstats| Q[Gene quantification]
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A-->|FastQC| W[Quality control]
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B-->|FastQC| X[Quality control]
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C-->|FastQC| Y[Quality control]
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... | ... | @@ -32,7 +32,7 @@ W-->|MultiQC| AA[Quality control file] |
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X-->|MultiQC| AA[Quality control file]
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Y-->|MultiQC| AA[Quality control file]
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Z-->|MultiQC| AA[Quality control file]
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Q-->|Python program| AB[Transcript quantification synthesis]
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Q-->|Python program| AB[Gene quantification synthesis]
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AC[Database index Kaiju]-->|kaiju MEM| AD[Taxonomic classification of reads]
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G-->|kaiju MEM| AD[Taxonomic classification of reads]
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AD-->|kaiju2krona| AE[Formatted files for krona generation]
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... | ... | |