-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
410 changed files
with
12,019 additions
and
0 deletions.
There are no files selected for viewing
Binary file not shown.
55 changes: 55 additions & 0 deletions
55
Study_cases/StarSignDNA_cases/config_mut_frac_0_mut_genomes_0_perfect_r_35000000_c_2500.yml
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| #Please check the parameters, and adjust them according to your project needs. | ||
|
|
||
| # Project name | ||
| PROJECT: IS-WES | ||
|
|
||
|
|
||
| # ================= General arguments ================== | ||
|
|
||
| NUM_SAMPLES: 1 | ||
| FRAG_REPLICATES: 1 | ||
| NCORE: 58 | ||
| SEED: "" | ||
| OUTPUT_DIRECTORY: "/usr/src/app/scratch/Output_data_7" | ||
| INPUT_DIRECTORY: "/usr/src/app/pipeline/input_data" | ||
| FASTA_FILE: "human_genome.fasta.gz" | ||
| SBS_SIGNATURES: "" | ||
|
|
||
| # ================== Configuration for 1defining_seq_and_mut ================== | ||
|
|
||
| MUT_CONTEXT: "" | ||
| TS_TV_RATIO: "" | ||
| VARIANT_PROBABILITY_TABLE: "" | ||
| NR_COPIES: "2500" | ||
| MULTIFASTA_COPIES: "" | ||
| MUT_GENOME_FRACTION: "" | ||
| FRACTION_POSITION: "" | ||
| MUTATION_RATE: "0" | ||
|
|
||
|
|
||
| # ================== Whole Human Exom or Specific probes ================== | ||
| PROBES_FASTA: "" | ||
| PROBES_BED: "xgen-exome-research-panel-v2-probes-hg38_short_all.bed" #probe binding coordinates | ||
| PROBES_TARGES: "xgen-exome-research-panel-v2-targets-hg38_short_all.bed" # regions which probes target | ||
|
|
||
| # ================== Configuration for Fragmentation ================== | ||
|
|
||
| FRAGMENT_FRACTION: "" | ||
| MIN_FRAGMENT_LENGTH: "250" | ||
| MAX_FRAGMENT_LENGTH: "1000" | ||
| MATCHING_LENGTH: "100" | ||
|
|
||
| # ================== Configuration for PCR ================== | ||
|
|
||
| K_PARAMETER_pcr: "0.3" | ||
| MIDPOINT_CYCLE: "20" | ||
| NUM_CYCLES: "8" | ||
|
|
||
| # ================= Sequencing Parameteres ================== | ||
|
|
||
| NUM_READS: "35000000" | ||
| MODE: "perfect" | ||
| ERROR_MODEL: "" | ||
| FASTA_GZ_OUTPUT: "--compress" | ||
| OPT_FRAG_MODE: "median" | ||
| K_PARAMETER_seq: "0.05" |
2 changes: 2 additions & 0 deletions
2
.../StarSignDNA_cases/config_mut_frac_0_mut_genomes_0_perfect_r_35000000_c_2500_seed_log.txt
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| Major Seed: 842969308 | ||
| Sample 1, Tech Replicate 1: Seed = 982448796 |
55 changes: 55 additions & 0 deletions
55
Study_cases/StarSignDNA_cases/config_mut_frac_0_mut_genomes_0_r_35000000_c_2500.yml
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| #Please check the parameters, and adjust them according to your project needs. | ||
|
|
||
| # Project name | ||
| PROJECT: IS-WES | ||
|
|
||
|
|
||
| # ================= General arguments ================== | ||
|
|
||
| NUM_SAMPLES: 1 | ||
| FRAG_REPLICATES: 1 | ||
| NCORE: 58 | ||
| SEED: "" | ||
| OUTPUT_DIRECTORY: "/usr/src/app/scratch/Output_data_7" | ||
| INPUT_DIRECTORY: "/usr/src/app/pipeline/input_data" | ||
| FASTA_FILE: "human_genome.fasta.gz" | ||
| SBS_SIGNATURES: "" | ||
|
|
||
| # ================== Configuration for 1defining_seq_and_mut ================== | ||
|
|
||
| MUT_CONTEXT: "" | ||
| TS_TV_RATIO: "" | ||
| VARIANT_PROBABILITY_TABLE: "" | ||
| NR_COPIES: "2500" | ||
| MULTIFASTA_COPIES: "" | ||
| MUT_GENOME_FRACTION: "" | ||
| FRACTION_POSITION: "" | ||
| MUTATION_RATE: "0" | ||
|
|
||
|
|
||
| # ================== Whole Human Exom or Specific probes ================== | ||
| PROBES_FASTA: "" | ||
| PROBES_BED: "xgen-exome-research-panel-v2-probes-hg38_short_all.bed" #probe binding coordinates | ||
| PROBES_TARGES: "xgen-exome-research-panel-v2-targets-hg38_short_all.bed" # regions which probes target | ||
|
|
||
| # ================== Configuration for Fragmentation ================== | ||
|
|
||
| FRAGMENT_FRACTION: "" | ||
| MIN_FRAGMENT_LENGTH: "250" | ||
| MAX_FRAGMENT_LENGTH: "1000" | ||
| MATCHING_LENGTH: "100" | ||
|
|
||
| # ================== Configuration for PCR ================== | ||
|
|
||
| K_PARAMETER_pcr: "0.3" | ||
| MIDPOINT_CYCLE: "20" | ||
| NUM_CYCLES: "8" | ||
|
|
||
| # ================= Sequencing Parameteres ================== | ||
|
|
||
| NUM_READS: "35000000" | ||
| MODE: "" | ||
| ERROR_MODEL: "novaseq" | ||
| FASTA_GZ_OUTPUT: "--compress" | ||
| OPT_FRAG_MODE: "median" | ||
| K_PARAMETER_seq: "0.05" |
2 changes: 2 additions & 0 deletions
2
Study_cases/StarSignDNA_cases/config_mut_frac_0_mut_genomes_0_r_35000000_c_2500_seed_log.txt
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| Major Seed: 388430262 | ||
| Sample 1, Tech Replicate 1: Seed = 1573206487 |
55 changes: 55 additions & 0 deletions
55
...es/StarSignDNA_cases/config_mut_frac_3_mut_genomes_08_sbs13_perfect_r_35000000_c_2500.yml
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| #Please check the parameters, and adjust them according to your project needs. | ||
|
|
||
| # Project name | ||
| PROJECT: IS-WES | ||
|
|
||
|
|
||
| # ================= General arguments ================== | ||
|
|
||
| NUM_SAMPLES: 1 | ||
| FRAG_REPLICATES: 1 | ||
| NCORE: 58 | ||
| SEED: "" | ||
| OUTPUT_DIRECTORY: "/usr/src/app/scratch/Output_data_7" | ||
| INPUT_DIRECTORY: "/usr/src/app/pipeline/input_data" | ||
| FASTA_FILE: "human_genome.fasta.gz" | ||
| SBS_SIGNATURES: "sbs13_short.csv" | ||
|
|
||
| # ================== Configuration for 1defining_seq_and_mut ================== | ||
|
|
||
| MUT_CONTEXT: "" | ||
| TS_TV_RATIO: "" | ||
| VARIANT_PROBABILITY_TABLE: "" | ||
| NR_COPIES: "2500" | ||
| MULTIFASTA_COPIES: "" | ||
| MUT_GENOME_FRACTION: "0.8" | ||
| FRACTION_POSITION: "0.03" | ||
| MUTATION_RATE: "" | ||
|
|
||
|
|
||
| # ================== Whole Human Exom or Specific probes ================== | ||
| PROBES_FASTA: "" | ||
| PROBES_BED: "xgen-exome-research-panel-v2-probes-hg38_short_all.bed" #probe binding coordinates | ||
| PROBES_TARGES: "xgen-exome-research-panel-v2-targets-hg38_short_all.bed" # regions which probes target | ||
|
|
||
| # ================== Configuration for Fragmentation ================== | ||
|
|
||
| FRAGMENT_FRACTION: "" | ||
| MIN_FRAGMENT_LENGTH: "250" | ||
| MAX_FRAGMENT_LENGTH: "1000" | ||
| MATCHING_LENGTH: "100" | ||
|
|
||
| # ================== Configuration for PCR ================== | ||
|
|
||
| K_PARAMETER_pcr: "0.3" | ||
| MIDPOINT_CYCLE: "20" | ||
| NUM_CYCLES: "8" | ||
|
|
||
| # ================= Sequencing Parameteres ================== | ||
|
|
||
| NUM_READS: "35000000" | ||
| MODE: "perfect" | ||
| ERROR_MODEL: "" | ||
| FASTA_GZ_OUTPUT: "--compress" | ||
| OPT_FRAG_MODE: "median" | ||
| K_PARAMETER_seq: "0.05" |
2 changes: 2 additions & 0 deletions
2
...gnDNA_cases/config_mut_frac_3_mut_genomes_08_sbs13_perfect_r_35000000_c_2500_seed_log.txt
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| Major Seed: 1281743083 | ||
| Sample 1, Tech Replicate 1: Seed = 820019690 |
55 changes: 55 additions & 0 deletions
55
Study_cases/StarSignDNA_cases/config_mut_frac_3_mut_genomes_08_sbs13_r_35000000_c_2500.yml
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| #Please check the parameters, and adjust them according to your project needs. | ||
|
|
||
| # Project name | ||
| PROJECT: IS-WES | ||
|
|
||
|
|
||
| # ================= General arguments ================== | ||
|
|
||
| NUM_SAMPLES: 1 | ||
| FRAG_REPLICATES: 1 | ||
| NCORE: 58 | ||
| SEED: "" | ||
| OUTPUT_DIRECTORY: "/usr/src/app/scratch/Output_data_7" | ||
| INPUT_DIRECTORY: "/usr/src/app/pipeline/input_data" | ||
| FASTA_FILE: "human_genome.fasta.gz" | ||
| SBS_SIGNATURES: "sbs13_short.csv" | ||
|
|
||
| # ================== Configuration for 1defining_seq_and_mut ================== | ||
|
|
||
| MUT_CONTEXT: "" | ||
| TS_TV_RATIO: "" | ||
| VARIANT_PROBABILITY_TABLE: "" | ||
| NR_COPIES: "2500" | ||
| MULTIFASTA_COPIES: "" | ||
| MUT_GENOME_FRACTION: "0.8" | ||
| FRACTION_POSITION: "0.03" | ||
| MUTATION_RATE: "" | ||
|
|
||
|
|
||
| # ================== Whole Human Exom or Specific probes ================== | ||
| PROBES_FASTA: "" | ||
| PROBES_BED: "xgen-exome-research-panel-v2-probes-hg38_short_all.bed" #probe binding coordinates | ||
| PROBES_TARGES: "xgen-exome-research-panel-v2-targets-hg38_short_all.bed" # regions which probes target | ||
|
|
||
| # ================== Configuration for Fragmentation ================== | ||
|
|
||
| FRAGMENT_FRACTION: "" | ||
| MIN_FRAGMENT_LENGTH: "250" | ||
| MAX_FRAGMENT_LENGTH: "1000" | ||
| MATCHING_LENGTH: "100" | ||
|
|
||
| # ================== Configuration for PCR ================== | ||
|
|
||
| K_PARAMETER_pcr: "0.3" | ||
| MIDPOINT_CYCLE: "20" | ||
| NUM_CYCLES: "8" | ||
|
|
||
| # ================= Sequencing Parameteres ================== | ||
|
|
||
| NUM_READS: "35000000" | ||
| MODE: "" | ||
| ERROR_MODEL: "novaseq" | ||
| FASTA_GZ_OUTPUT: "--compress" | ||
| OPT_FRAG_MODE: "median" | ||
| K_PARAMETER_seq: "0.05" |
2 changes: 2 additions & 0 deletions
2
...s/StarSignDNA_cases/config_mut_frac_3_mut_genomes_08_sbs13_r_35000000_c_2500_seed_log.txt
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| Major Seed: 1418539074 | ||
| Sample 1, Tech Replicate 1: Seed = 423598893 |
55 changes: 55 additions & 0 deletions
55
...s/StarSignDNA_cases/config_mut_frac_3_mut_genomes_08_sbs17b_perfect_r_35000000_c_2500.yml
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| #Please check the parameters, and adjust them according to your project needs. | ||
|
|
||
| # Project name | ||
| PROJECT: IS-WES | ||
|
|
||
|
|
||
| # ================= General arguments ================== | ||
|
|
||
| NUM_SAMPLES: 1 | ||
| FRAG_REPLICATES: 1 | ||
| NCORE: 58 | ||
| SEED: "" | ||
| OUTPUT_DIRECTORY: "/usr/src/app/scratch/Output_data_7" | ||
| INPUT_DIRECTORY: "/usr/src/app/pipeline/input_data" | ||
| FASTA_FILE: "human_genome.fasta.gz" | ||
| SBS_SIGNATURES: "sbs17b_short.csv" | ||
|
|
||
| # ================== Configuration for 1defining_seq_and_mut ================== | ||
|
|
||
| MUT_CONTEXT: "" | ||
| TS_TV_RATIO: "" | ||
| VARIANT_PROBABILITY_TABLE: "" | ||
| NR_COPIES: "2500" | ||
| MULTIFASTA_COPIES: "" | ||
| MUT_GENOME_FRACTION: "0.8" | ||
| FRACTION_POSITION: "0.03" | ||
| MUTATION_RATE: "" | ||
|
|
||
|
|
||
| # ================== Whole Human Exom or Specific probes ================== | ||
| PROBES_FASTA: "" | ||
| PROBES_BED: "xgen-exome-research-panel-v2-probes-hg38_short_all.bed" #probe binding coordinates | ||
| PROBES_TARGES: "xgen-exome-research-panel-v2-targets-hg38_short_all.bed" # regions which probes target | ||
|
|
||
| # ================== Configuration for Fragmentation ================== | ||
|
|
||
| FRAGMENT_FRACTION: "" | ||
| MIN_FRAGMENT_LENGTH: "250" | ||
| MAX_FRAGMENT_LENGTH: "1000" | ||
| MATCHING_LENGTH: "100" | ||
|
|
||
| # ================== Configuration for PCR ================== | ||
|
|
||
| K_PARAMETER_pcr: "0.3" | ||
| MIDPOINT_CYCLE: "20" | ||
| NUM_CYCLES: "8" | ||
|
|
||
| # ================= Sequencing Parameteres ================== | ||
|
|
||
| NUM_READS: "35000000" | ||
| MODE: "perfect" | ||
| ERROR_MODEL: "" | ||
| FASTA_GZ_OUTPUT: "--compress" | ||
| OPT_FRAG_MODE: "median" | ||
| K_PARAMETER_seq: "0.05" |
2 changes: 2 additions & 0 deletions
2
...nDNA_cases/config_mut_frac_3_mut_genomes_08_sbs17b_perfect_r_35000000_c_2500_seed_log.txt
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| Major Seed: 1376117560 | ||
| Sample 1, Tech Replicate 1: Seed = 379195045 |
55 changes: 55 additions & 0 deletions
55
Study_cases/StarSignDNA_cases/config_mut_frac_3_mut_genomes_08_sbs17b_r_35000000_c_2500.yml
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| #Please check the parameters, and adjust them according to your project needs. | ||
|
|
||
| # Project name | ||
| PROJECT: IS-WES | ||
|
|
||
|
|
||
| # ================= General arguments ================== | ||
|
|
||
| NUM_SAMPLES: 1 | ||
| FRAG_REPLICATES: 1 | ||
| NCORE: 58 | ||
| SEED: "" | ||
| OUTPUT_DIRECTORY: "/usr/src/app/scratch/Output_data_7" | ||
| INPUT_DIRECTORY: "/usr/src/app/pipeline/input_data" | ||
| FASTA_FILE: "human_genome.fasta.gz" | ||
| SBS_SIGNATURES: "sbs17b_short.csv" | ||
|
|
||
| # ================== Configuration for 1defining_seq_and_mut ================== | ||
|
|
||
| MUT_CONTEXT: "" | ||
| TS_TV_RATIO: "" | ||
| VARIANT_PROBABILITY_TABLE: "" | ||
| NR_COPIES: "2500" | ||
| MULTIFASTA_COPIES: "" | ||
| MUT_GENOME_FRACTION: "0.8" | ||
| FRACTION_POSITION: "0.03" | ||
| MUTATION_RATE: "" | ||
|
|
||
|
|
||
| # ================== Whole Human Exom or Specific probes ================== | ||
| PROBES_FASTA: "" | ||
| PROBES_BED: "xgen-exome-research-panel-v2-probes-hg38_short_all.bed" #probe binding coordinates | ||
| PROBES_TARGES: "xgen-exome-research-panel-v2-targets-hg38_short_all.bed" # regions which probes target | ||
|
|
||
| # ================== Configuration for Fragmentation ================== | ||
|
|
||
| FRAGMENT_FRACTION: "" | ||
| MIN_FRAGMENT_LENGTH: "250" | ||
| MAX_FRAGMENT_LENGTH: "1000" | ||
| MATCHING_LENGTH: "100" | ||
|
|
||
| # ================== Configuration for PCR ================== | ||
|
|
||
| K_PARAMETER_pcr: "0.3" | ||
| MIDPOINT_CYCLE: "20" | ||
| NUM_CYCLES: "8" | ||
|
|
||
| # ================= Sequencing Parameteres ================== | ||
|
|
||
| NUM_READS: "35000000" | ||
| MODE: "" | ||
| ERROR_MODEL: "novaseq" | ||
| FASTA_GZ_OUTPUT: "--compress" | ||
| OPT_FRAG_MODE: "median" | ||
| K_PARAMETER_seq: "0.05" |
2 changes: 2 additions & 0 deletions
2
.../StarSignDNA_cases/config_mut_frac_3_mut_genomes_08_sbs17b_r_35000000_c_2500_seed_log.txt
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| Major Seed: 2068062533 | ||
| Sample 1, Tech Replicate 1: Seed = 1262637086 |
Oops, something went wrong.