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"
}