Skip to content
Open
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Original file line number Diff line number Diff line change
@@ -0,0 +1,88 @@
{
"tool": "Trim Galore",
"schema_version": 1,
"trim_galore_version": "2.1.0-beta.5",
"input_filenames": ["BS-seq_10K_R1.fastq.gz", "BS-seq_10K_R2.fastq.gz"],
"mode": "paired-end",
"read_number": 1,
"command_line": "/Users/fkrueger/Github/TrimGalore/target/release/trim_galore --paired BS-seq_10K_R1.fastq.gz BS-seq_10K_R2.fastq.gz",
"parameters": {
"quality_cutoff": 20,
"adapters": [{ "name": "Illumina", "sequence": "AGATCGGAAGAGC" }],
"adapters_r2": [],
"times": 1,
"error_rate": 0.1,
"stringency": 1,
"length_cutoff": 20,
"max_length": null,
"phred_encoding": 33,
"trim_n": false,
"nextseq": false,
"rrbs": false,
"non_directional": false,
"poly_a": false,
"poly_g": false,
"clip_r1": null,
"clip_r2": null,
"three_prime_clip_r1": null,
"three_prime_clip_r2": null,
"max_n": null,
"discard_untrimmed": false,
"consider_already_trimmed": null
},
"read_processing": {
"total_reads": 10000,
"reads_with_adapter": 3775,
"reads_written": 9996,
"reads_too_short": 4,
"reads_too_long": 0,
"reads_too_many_n": 0,
"reads_discarded_untrimmed": 0
},
"basepair_processing": {
"total_bp_processed": 650000,
"quality_trimmed_bp": 0,
"total_bp_written": 644525
},
"adapter_trimming": [
{
"name": "Illumina",
"sequence": "AGATCGGAAGAGC",
"type": "regular 3'",
"length": 13,
"times_trimmed": 3775,
"length_distribution": {
"1": 2753,
"2": 703,
"3": 223,
"4": 86,
"5": 2,
"6": 1,
"7": 1,
"10": 2,
"65": 4
}
}
],
"poly_a_trimming": {
"reads_trimmed": 0,
"bases_removed": 0
},
"poly_g_trimming": {
"reads_trimmed": 0,
"bases_removed": 0
},
"rrbs": {
"trimmed_3prime": 0,
"trimmed_5prime": 0,
"r2_clipped_5prime": 0
},
"pair_validation": {
"pairs_analyzed": 10000,
"pairs_removed": 4,
"pairs_removed_n": 0,
"pairs_removed_too_long": 0,
"r1_unpaired": 0,
"r2_unpaired": 0
}
}
Original file line number Diff line number Diff line change
@@ -0,0 +1,85 @@
{
"tool": "Trim Galore",
"schema_version": 1,
"trim_galore_version": "2.1.0-beta.5",
"input_filenames": ["BS-seq_10K_R1.fastq.gz", "BS-seq_10K_R2.fastq.gz"],
"mode": "paired-end",
"read_number": 2,
"command_line": "/Users/fkrueger/Github/TrimGalore/target/release/trim_galore --paired BS-seq_10K_R1.fastq.gz BS-seq_10K_R2.fastq.gz",
"parameters": {
"quality_cutoff": 20,
"adapters": [{ "name": "Illumina", "sequence": "AGATCGGAAGAGC" }],
"adapters_r2": [],
"times": 1,
"error_rate": 0.1,
"stringency": 1,
"length_cutoff": 20,
"max_length": null,
"phred_encoding": 33,
"trim_n": false,
"nextseq": false,
"rrbs": false,
"non_directional": false,
"poly_a": false,
"poly_g": false,
"clip_r1": null,
"clip_r2": null,
"three_prime_clip_r1": null,
"three_prime_clip_r2": null,
"max_n": null,
"discard_untrimmed": false,
"consider_already_trimmed": null
},
"read_processing": {
"total_reads": 10000,
"reads_with_adapter": 4882,
"reads_written": 9996,
"reads_too_short": 4,
"reads_too_long": 0,
"reads_too_many_n": 0,
"reads_discarded_untrimmed": 0
},
"basepair_processing": {
"total_bp_processed": 650000,
"quality_trimmed_bp": 0,
"total_bp_written": 644815
},
"adapter_trimming": [
{
"name": "Illumina",
"sequence": "AGATCGGAAGAGC",
"type": "regular 3'",
"length": 13,
"times_trimmed": 4882,
"length_distribution": {
"1": 4866,
"2": 8,
"3": 2,
"4": 3,
"7": 1,
"10": 2
}
}
],
"poly_a_trimming": {
"reads_trimmed": 0,
"bases_removed": 0
},
"poly_g_trimming": {
"reads_trimmed": 0,
"bases_removed": 0
},
"rrbs": {
"trimmed_3prime": 0,
"trimmed_5prime": 0,
"r2_clipped_5prime": 0
},
"pair_validation": {
"pairs_analyzed": 10000,
"pairs_removed": 4,
"pairs_removed_n": 0,
"pairs_removed_too_long": 0,
"r1_unpaired": 0,
"r2_unpaired": 0
}
}
215 changes: 215 additions & 0 deletions data/modules/trim_galore/sample_R1.fastq.gz_trimming_report.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,215 @@
{
"tool": "Trim Galore",
"schema_version": 1,
"trim_galore_version": "2.1.0-beta.5",
"input_filenames": ["sample.fastq.gz"],
"mode": "single-end",
"read_number": 1,
"command_line": "/Users/fkrueger/Github/TrimGalore/target/release/trim_galore sample.fastq.gz",
"parameters": {
"quality_cutoff": 20,
"adapters": [{ "name": "Illumina", "sequence": "AGATCGGAAGAGC" }],
"adapters_r2": [],
"times": 1,
"error_rate": 0.1,
"stringency": 1,
"length_cutoff": 20,
"max_length": null,
"phred_encoding": 33,
"trim_n": false,
"nextseq": false,
"rrbs": false,
"non_directional": false,
"poly_a": false,
"poly_g": false,
"clip_r1": null,
"clip_r2": null,
"three_prime_clip_r1": null,
"three_prime_clip_r2": null,
"max_n": null,
"discard_untrimmed": false,
"consider_already_trimmed": null
},
"read_processing": {
"total_reads": 10000,
"reads_with_adapter": 6382,
"reads_written": 9923,
"reads_too_short": 77,
"reads_too_long": 0,
"reads_too_many_n": 0,
"reads_discarded_untrimmed": 0
},
"basepair_processing": {
"total_bp_processed": 1500000,
"quality_trimmed_bp": 13264,
"total_bp_written": 1300218
},
"adapter_trimming": [
{
"name": "Illumina",
"sequence": "AGATCGGAAGAGC",
"type": "regular 3'",
"length": 13,
"times_trimmed": 6382,
"length_distribution": {
"1": 2549,
"2": 216,
"3": 85,
"4": 59,
"5": 43,
"6": 42,
"7": 44,
"8": 41,
"9": 57,
"10": 53,
"11": 41,
"12": 46,
"13": 26,
"14": 52,
"15": 43,
"16": 41,
"17": 46,
"18": 50,
"19": 54,
"20": 38,
"21": 43,
"22": 35,
"23": 44,
"24": 32,
"25": 28,
"26": 42,
"27": 40,
"28": 41,
"29": 29,
"30": 51,
"31": 39,
"32": 31,
"33": 32,
"34": 43,
"35": 40,
"36": 41,
"37": 43,
"38": 39,
"39": 39,
"40": 33,
"41": 29,
"42": 38,
"43": 40,
"44": 32,
"45": 42,
"46": 33,
"47": 18,
"48": 38,
"49": 30,
"50": 24,
"51": 40,
"52": 33,
"53": 34,
"54": 24,
"55": 36,
"56": 33,
"57": 31,
"58": 34,
"59": 31,
"60": 24,
"61": 28,
"62": 31,
"63": 28,
"64": 13,
"65": 19,
"66": 25,
"67": 28,
"68": 28,
"69": 31,
"70": 16,
"71": 29,
"72": 30,
"73": 30,
"74": 24,
"75": 24,
"76": 28,
"77": 19,
"78": 33,
"79": 29,
"80": 30,
"81": 33,
"82": 41,
"83": 69,
"84": 64,
"85": 68,
"86": 53,
"87": 24,
"88": 34,
"89": 16,
"90": 14,
"91": 13,
"92": 10,
"93": 19,
"94": 9,
"95": 9,
"96": 13,
"97": 12,
"98": 10,
"99": 13,
"100": 12,
"101": 12,
"102": 9,
"103": 12,
"104": 13,
"105": 8,
"106": 11,
"107": 12,
"108": 11,
"109": 7,
"110": 5,
"111": 10,
"112": 17,
"113": 4,
"114": 7,
"115": 9,
"116": 6,
"117": 6,
"118": 11,
"119": 9,
"120": 4,
"121": 6,
"122": 6,
"123": 5,
"124": 10,
"125": 9,
"126": 6,
"127": 6,
"128": 10,
"129": 6,
"130": 4,
"131": 7,
"132": 6,
"133": 2,
"134": 5,
"135": 2,
"136": 2,
"137": 1,
"138": 2,
"139": 2,
"140": 3,
"141": 1,
"142": 2,
"149": 2
}
}
],
"poly_a_trimming": {
"reads_trimmed": 0,
"bases_removed": 0
},
"poly_g_trimming": {
"reads_trimmed": 0,
"bases_removed": 0
},
"rrbs": {
"trimmed_3prime": 0,
"trimmed_5prime": 0,
"r2_clipped_5prime": 0
},
"pair_validation": null
}