Align Report ------------------------------------------------------------------------ Align Report: Fields ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ==================================================================== ============== Name Data Type ==================================================================== ============== Name of Sample str Use demultiplexed mode bool Use paired-end mode bool Phred score encoding in FASTQ and SAM/BAM/CRAM files int Run FastQC on the initial and trimmed FASTQ files bool Trim reads with Cutadapt before alignment bool Phred score for read 1 quality trimming with Cutadapt int Phred score for read 2 quality trimming with Cutadapt int 5' adapter for read 1 adapter trimming with Cutadapt list[str] 3' adapter for read 1 adapter trimming with Cutadapt list[str] 5' adapter for read 2 adapter trimming with Cutadapt list[str] 3' adapter for read 2 adapter trimming with Cutadapt list[str] Minimum overlap of read and adapter during trimming with Cutadapt int Error tolerance for adapters during trimming with Cutadapt float Allow indels in adapters during trimming with Cutadapt bool Trim high-quality Gs from 3' end during trimming with Cutadapt bool Discard reads in which an adapter was found by Cutadapt bool Discard reads in which no adapter was found by Cutadapt bool Minimum length of a read to keep it after trimming with Cutadapt int Run Bowtie2 in local mode bool Output discordant alignments from Bowtie2 bool Attempt to align individual mates of unaligned pairs with Bowtie2 bool Treat dovetailed mate pairs as concordant with Bowtie2 bool Treat nested mate pairs as concordant with Bowtie2 bool Minimum score for a valid alignment with Bowtie2 str Minimum fragment length for valid paired-end alignments with Bowtie2 int Maximum fragment length for valid paired-end alignments with Bowtie2 int Minimum distance of an indel from the end of a read with Bowtie2 int Seed length for Bowtie2 int Seed interval for Bowtie2 str Maximum number of consecutive failed seed extensions with Bowtie2 int Maximum number of re-seeding attempts with Bowtie2 int Width of padding on alignment matrix (to allow indels) with Bowtie2 int Valid orientations of paired-end mates with Bowtie2 str Output unaligned reads from Bowtie2 to a FASTQ file bool Minimum mapping quality to keep an aligned read from Bowtie2 int Number of reads initially int Number of reads after trimming int Number of reads after alignment dict[str, int] Number of reads after filtering dict[str, int] Number of reads aligned by reference dict[str, int] Branches list[str] Time Began str Time Ended str Time Taken (minutes) float Version of SEISMIC-RNA str ==================================================================== ============== Align Report: Example ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ :: { "Name of Sample": "ldi", "Use demultiplexed mode": false, "Use paired-end mode": true, "Phred score encoding in FASTQ and SAM/BAM/CRAM files": 33, "Run FastQC on the initial and trimmed FASTQ files": true, "Trim reads with Cutadapt before alignment": true, "Phred score for read 1 quality trimming with Cutadapt": 25, "Phred score for read 2 quality trimming with Cutadapt": 25, "5' adapter for read 1 adapter trimming with Cutadapt": [ "GCTCTTCCGATCT" ], "3' adapter for read 1 adapter trimming with Cutadapt": [ "AGATCGGAAGAGC" ], "5' adapter for read 2 adapter trimming with Cutadapt": [ "GCTCTTCCGATCT" ], "3' adapter for read 2 adapter trimming with Cutadapt": [ "AGATCGGAAGAGC" ], "Minimum overlap of read and adapter during trimming with Cutadapt": 6, "Error tolerance for adapters during trimming with Cutadapt": 0.1, "Allow indels in adapters during trimming with Cutadapt": true, "Trim high-quality Gs from 3' end during trimming with Cutadapt": false, "Discard reads in which an adapter was found by Cutadapt": false, "Discard reads in which no adapter was found by Cutadapt": false, "Minimum length of a read to keep it after trimming with Cutadapt": 20, "Run Bowtie2 in local mode": true, "Output discordant alignments from Bowtie2": false, "Attempt to align individual mates of unaligned pairs with Bowtie2": false, "Treat dovetailed mate pairs as concordant with Bowtie2": false, "Treat nested mate pairs as concordant with Bowtie2": true, "Minimum score for a valid alignment with Bowtie2": "L,1,0.5", "Minimum fragment length for valid paired-end alignments with Bowtie2": 0, "Maximum fragment length for valid paired-end alignments with Bowtie2": 600, "Minimum distance of an indel from the end of a read with Bowtie2": 4, "Seed length for Bowtie2": 20, "Seed interval for Bowtie2": "L,1,0.1", "Maximum number of consecutive failed seed extensions with Bowtie2": 4, "Maximum number of re-seeding attempts with Bowtie2": 2, "Width of padding on alignment matrix (to allow indels) with Bowtie2": 2, "Valid orientations of paired-end mates with Bowtie2": "fr", "Output unaligned reads from Bowtie2 to a FASTQ file": true, "Minimum mapping quality to keep an aligned read from Bowtie2": 25, "Number of reads initially": 566520, "Number of reads after trimming": 565068, "Number of reads after alignment": { "reads, were paired": 565068, "reads, were paired, aligned concordantly 0 times": 2613, "reads, were paired, aligned concordantly exactly 1 time": 562448, "reads, were paired, aligned concordantly >1 times": 7 }, "Number of reads after filtering": { "paired-end, both mates mapped": 562325, "paired-end, one mate unmapped": 0 }, "Number of reads aligned by reference": { "sars2_1799": 562325 }, "Branches": [], "Time Began": "2023-11-10 at 20:16:29", "Time Ended": "2023-11-10 at 20:17:39", "Time Taken (minutes)": 1.16, "Version of SEISMIC-RNA": "0.9.3" }