The prerequisite files for running each of the five analysis steps in gmRAD with default parameters and the corresponding main result files each with a description.
| Step . | Prerequisite Files . | Main Result Files . | Description . |
|---|---|---|---|
| 1 | parameter.ini | femaleparent.cls | The first read ids and their consensus within a cluster for the female parent. |
| maleparent.cls | The similar file for the male parent. | ||
| 2 | parameter.ini | femaleClusterRef.fasta | The reference sequences built from the first and second reads within each cluster for the female parent. |
| femaleparent.cls | |||
| maleparent.cls | femaleClusterRef.fasta | The similar file for the male parent. | |
| 3 | parameter.ini | female_gtp.loc | SNP catalog based on the female reference. |
| femaleClusterRef.fasta | female.gtp | The female and male genotypes based on the female reference. | |
| maleClusterRef.fasta | male_gtp.loc | SNP catalog based on the female reference | |
| male.gtp | The female and male genotypes based on the male reference. | ||
| 4 | parameter.ini | FemaleRefRawSNPs.txt | SNP genotypes across all individuals based on the female reference. |
| female.gtp | |||
| female_gtp.loc | MaleRefRawSNPs.txt | SNP genotypes across all individuals based on the male reference | |
| male.gtp | |||
| male_gtp.loc | |||
| 5 | parameter.ini | FemaleRefRawSNPs2.txt | Genotype counts, p values for chi-squared test and genotype notations for each record in |
| FemaleRefRawSNPs.txt | FemaleRefRawSNPs.txt. | ||
| MaleRefRawSNPs.txt | MaleRefRawSNPs2.txt | The similar file from MaleRefRawSNPs.txt. | |
| aaxab_pct90pv01.txt | The final genotype data segregating in aaxab. | ||
| aaxbc_pct90pv01.txt | The final genotype data segregating in aaxbc. | ||
| abxaa_pct90pv01.txt | The final genotype data segregating in abxaa. | ||
| abxab_pct90pv01.txt | The final genotype data segregating in abxab. | ||
| abxac_pct90pv01.txt | The final genotype data segregating in abxac. | ||
| abxcc_pct90pv01.txt | The final genotype data segregating in abxcc. | ||
| abxcd_pct90pv01.txt | The final genotype data segregating in abxcd | ||
| all_pct90pv01_joinmap.xlsx | All final genotype data formatted as input to the software JoinMap. |
| Step . | Prerequisite Files . | Main Result Files . | Description . |
|---|---|---|---|
| 1 | parameter.ini | femaleparent.cls | The first read ids and their consensus within a cluster for the female parent. |
| maleparent.cls | The similar file for the male parent. | ||
| 2 | parameter.ini | femaleClusterRef.fasta | The reference sequences built from the first and second reads within each cluster for the female parent. |
| femaleparent.cls | |||
| maleparent.cls | femaleClusterRef.fasta | The similar file for the male parent. | |
| 3 | parameter.ini | female_gtp.loc | SNP catalog based on the female reference. |
| femaleClusterRef.fasta | female.gtp | The female and male genotypes based on the female reference. | |
| maleClusterRef.fasta | male_gtp.loc | SNP catalog based on the female reference | |
| male.gtp | The female and male genotypes based on the male reference. | ||
| 4 | parameter.ini | FemaleRefRawSNPs.txt | SNP genotypes across all individuals based on the female reference. |
| female.gtp | |||
| female_gtp.loc | MaleRefRawSNPs.txt | SNP genotypes across all individuals based on the male reference | |
| male.gtp | |||
| male_gtp.loc | |||
| 5 | parameter.ini | FemaleRefRawSNPs2.txt | Genotype counts, p values for chi-squared test and genotype notations for each record in |
| FemaleRefRawSNPs.txt | FemaleRefRawSNPs.txt. | ||
| MaleRefRawSNPs.txt | MaleRefRawSNPs2.txt | The similar file from MaleRefRawSNPs.txt. | |
| aaxab_pct90pv01.txt | The final genotype data segregating in aaxab. | ||
| aaxbc_pct90pv01.txt | The final genotype data segregating in aaxbc. | ||
| abxaa_pct90pv01.txt | The final genotype data segregating in abxaa. | ||
| abxab_pct90pv01.txt | The final genotype data segregating in abxab. | ||
| abxac_pct90pv01.txt | The final genotype data segregating in abxac. | ||
| abxcc_pct90pv01.txt | The final genotype data segregating in abxcc. | ||
| abxcd_pct90pv01.txt | The final genotype data segregating in abxcd | ||
| all_pct90pv01_joinmap.xlsx | All final genotype data formatted as input to the software JoinMap. |
The prerequisite files for running each of the five analysis steps in gmRAD with default parameters and the corresponding main result files each with a description.
| Step . | Prerequisite Files . | Main Result Files . | Description . |
|---|---|---|---|
| 1 | parameter.ini | femaleparent.cls | The first read ids and their consensus within a cluster for the female parent. |
| maleparent.cls | The similar file for the male parent. | ||
| 2 | parameter.ini | femaleClusterRef.fasta | The reference sequences built from the first and second reads within each cluster for the female parent. |
| femaleparent.cls | |||
| maleparent.cls | femaleClusterRef.fasta | The similar file for the male parent. | |
| 3 | parameter.ini | female_gtp.loc | SNP catalog based on the female reference. |
| femaleClusterRef.fasta | female.gtp | The female and male genotypes based on the female reference. | |
| maleClusterRef.fasta | male_gtp.loc | SNP catalog based on the female reference | |
| male.gtp | The female and male genotypes based on the male reference. | ||
| 4 | parameter.ini | FemaleRefRawSNPs.txt | SNP genotypes across all individuals based on the female reference. |
| female.gtp | |||
| female_gtp.loc | MaleRefRawSNPs.txt | SNP genotypes across all individuals based on the male reference | |
| male.gtp | |||
| male_gtp.loc | |||
| 5 | parameter.ini | FemaleRefRawSNPs2.txt | Genotype counts, p values for chi-squared test and genotype notations for each record in |
| FemaleRefRawSNPs.txt | FemaleRefRawSNPs.txt. | ||
| MaleRefRawSNPs.txt | MaleRefRawSNPs2.txt | The similar file from MaleRefRawSNPs.txt. | |
| aaxab_pct90pv01.txt | The final genotype data segregating in aaxab. | ||
| aaxbc_pct90pv01.txt | The final genotype data segregating in aaxbc. | ||
| abxaa_pct90pv01.txt | The final genotype data segregating in abxaa. | ||
| abxab_pct90pv01.txt | The final genotype data segregating in abxab. | ||
| abxac_pct90pv01.txt | The final genotype data segregating in abxac. | ||
| abxcc_pct90pv01.txt | The final genotype data segregating in abxcc. | ||
| abxcd_pct90pv01.txt | The final genotype data segregating in abxcd | ||
| all_pct90pv01_joinmap.xlsx | All final genotype data formatted as input to the software JoinMap. |
| Step . | Prerequisite Files . | Main Result Files . | Description . |
|---|---|---|---|
| 1 | parameter.ini | femaleparent.cls | The first read ids and their consensus within a cluster for the female parent. |
| maleparent.cls | The similar file for the male parent. | ||
| 2 | parameter.ini | femaleClusterRef.fasta | The reference sequences built from the first and second reads within each cluster for the female parent. |
| femaleparent.cls | |||
| maleparent.cls | femaleClusterRef.fasta | The similar file for the male parent. | |
| 3 | parameter.ini | female_gtp.loc | SNP catalog based on the female reference. |
| femaleClusterRef.fasta | female.gtp | The female and male genotypes based on the female reference. | |
| maleClusterRef.fasta | male_gtp.loc | SNP catalog based on the female reference | |
| male.gtp | The female and male genotypes based on the male reference. | ||
| 4 | parameter.ini | FemaleRefRawSNPs.txt | SNP genotypes across all individuals based on the female reference. |
| female.gtp | |||
| female_gtp.loc | MaleRefRawSNPs.txt | SNP genotypes across all individuals based on the male reference | |
| male.gtp | |||
| male_gtp.loc | |||
| 5 | parameter.ini | FemaleRefRawSNPs2.txt | Genotype counts, p values for chi-squared test and genotype notations for each record in |
| FemaleRefRawSNPs.txt | FemaleRefRawSNPs.txt. | ||
| MaleRefRawSNPs.txt | MaleRefRawSNPs2.txt | The similar file from MaleRefRawSNPs.txt. | |
| aaxab_pct90pv01.txt | The final genotype data segregating in aaxab. | ||
| aaxbc_pct90pv01.txt | The final genotype data segregating in aaxbc. | ||
| abxaa_pct90pv01.txt | The final genotype data segregating in abxaa. | ||
| abxab_pct90pv01.txt | The final genotype data segregating in abxab. | ||
| abxac_pct90pv01.txt | The final genotype data segregating in abxac. | ||
| abxcc_pct90pv01.txt | The final genotype data segregating in abxcc. | ||
| abxcd_pct90pv01.txt | The final genotype data segregating in abxcd | ||
| all_pct90pv01_joinmap.xlsx | All final genotype data formatted as input to the software JoinMap. |
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