How to call ReadSimulator: For a better overview, we list the individual parameters of the Read Simulator here again, including their default values and whether they are mandatory or optional.
Mandatory Parameters -fasta: Fasta file from which the reads are simulated. -fidx: Index file for the Fasta file. -gtf: Genomic annotations. -length: Desired length of the reads. -gene_id: Gene ID of the desired gene. -frlength: Average fragment length from which the reads are formed. -SD: Standard deviation for the formation of the fragment length. -od: Directory in which the fastaq files, the read mapping info, and the additional info are placed. Optional Parameters -readcounts: File containing the desired genes, their transcripts, and the number of reads, default: empty file. -transcript_count_for_gene: Number of transcripts selected for the specified gene to simulate, default: 1 transcript. -total_read_count: Number of reads for the specified gene, default: 100 reads.
-non_unique_frq: Probability that a read is completely or partially in an overlapping region, default: 50%. -overlap_on_more_than_1_T: Allows to generate reads that are completely or partially in an overlapping region that exists on multiple transcripts, default: false. -minoverlapsize: Allows to generate reads that are completely or partially in an overlapping region that have a certain size, which increases the probability that the read is completely in the overlapping region, default: 0.
-dot_mutation_rate: Probability of a point mutation for bases A,C,G,T, default: 0.0, 0.0, 0.0, 0.0. -insertion_mutation_rate: Probability of an insertion for bases A,C,G,T, default: 0.0, 0.0, 0.0, 0.0. -deletion_mutation_rate: Probability of a deletion for bases A,C,G,T, default: 0.0, 0.0, 0.0, 0.0. -junction_mutation_rate: Probability of a point mutation at exon boundaries, default: 0. -junction_size: Size of the region on which the junction mutation is formed, default: 3. -sequence_error_rate: Probability of a sequencing error, default: 0.01%.
-biological: Selects fragment positions as biologically accurate as possible. -bio_file: File path to the biological data. (HUMAN GTF3.8)
For CCR9 the gene_id is ENSG00000173585 total_transcript_count 4 For FYCO1 the gene_id is ENSG00000163820 total_transcript_count 5 For HIVEP3 the gene_id is ENSG00000127124 total_transcript_count 7 For LZTFL1 the gene_id is ENSG00000163818 total_transcript_count 15 For SLAMF1 the gene_id is ENSG00000117090 total_transcript_count 3 For SLAMF7 the gene_id is ENSG00000026751 total_transcript_count 11