Organization Structure
To start:
Current Directory{ Pipeline.py VSGFunctions.py [SequencingFile1].fastq [SequencingFile2].fastq }
When Finished:
Current Directory{ Pipeline.py VSGFunctions.py [SequencingFile1].fastq [SequencingFile2].fastq [Y-M-D-H_M]-[OptionalDescriptiveHeaderNames]{ # "Header" [SequencingFile1]{ [SequencingFile1]_trimmed2.fq } [SequencingFile2]{ [SequencingFile2]_trimmed2.fq }
[Header]_[SequencingFile1]_contig.fa
[Header]_[SequencingFile1]_orf_clean.fa
[Header]_[SequencingFile1]_orf_trans_clean.fa
[Header]_[SequencingFile1]_orf_trans.fa
[Header]_[SequencingFile1]_orf_VSGs_scores.txt
[Header]_[SequencingFile1]_orf_VSGs.fa
[Header]_[SequencingFile1]_orf.fa
[Header]_[SequencingFile2]_contig.fa
[Header]_[SequencingFile2]_orf_clean.fa
[Header]_[SequencingFile2]_orf_trans_clean.fa
[Header]_[SequencingFile2]_orf_trans.fa
[Header]_[SequencingFile2]_orf_VSGs_scores.txt
[Header]_[SequencingFile2]_orf_VSGs.fa
[Header]_[SequencingFile2]_orf.fa
[Header]_orf_VSGs_merged.fa
[Header]_orf_VSGs.fa
[Header]_[SequencingFile1]_orf.xml
[Header]_[SequencingFile2]_orf.xml
[SequencingFile1]_MULTo.txt
[SequencingFile1]_Trinity.Trinity.fasta
[SequencingFile2]_MULTo.txt
[SequencingFile2]_Trinity.Trinity.fasta
[Header]_orf_VSGs_merged.fa.clstr
[SequencingFile1]_align.sam
[SequencingFile2]_align.sam
}
}