complete_clusters_output
Gal Horesh edited this page Mar 6, 2019
·
2 revisions
File names:
| order | file names |
|---|---|
| upstream | <partner>U_<hit>H |
| downstream | <hit>H_<partner>D |
| both | <partner>U_<hit>H_<partner>D |
| either |
<partner>P_<hit>H or <hit>H_<partner>P or <partner>P_<hit>H_<partner>P
|
Output format:
| Column | Name | Description | Notes |
|---|---|---|---|
| 1 | Strain | Name of genome | |
| 2 | Upstream_Cluster | If found, cluster of the upstream ORF to this hit | Missing if using order downstream
|
| 3 | Downstream_Cluster | If found, cluster of the downstream ORF to this hit | Missing if using order upstream
|
| 4 | Domain | Highest scoring HMM profile in this hit | |
| 5 | HMMER_score | Score returned by hmmscan | |
| 6 | Contig | The identifier of the contig of this hit | |
| 7 | Strand | Strand of the hit | |
| 8 | Hit_length | Length of the hit (aa) | |
| 9 | Hit_start | Start of hit sequence on the contig | |
| 10 | Hit_stop | Stop of hit sequence on the contig | |
| 11 | Upstream_length | Length of upstream ORF if found (aa) | Missing if using order downstream
|
| 12 | Upstream_delta | Distance/overlap between upstream ORF and hit, if found (bp) | Missing if using order downstream
|
| 13 | Upstream_start | Start of upstream ORF on contig, if found | Missing if using order downstream
|
| 14 | Upstream_stop | Stop of upstream ORF on contig, if found | Missing if using order downstream
|
| 15 | Downstream_length | Length of downstream ORF if found (aa) | Missing if using order upstream
|
| 16 | Downstream_delta | Distance/overlap between hit and downstream ORF if found (bp) | Missing if using order upstream
|
| 17 | Downstream_start | Start of downstream ORF on the contig if found | Missing if using order upstream
|
| 18 | Downstream_stop | Stop of downstream ORF on the contig if found | Missing if using order upstream
|
| 19 | Hit | Hit sequence | |
| 20 | Upstream | Upstream ORF sequence (if found) | Missing if using order downstream
|
| 21 | Downstream | Downstream ORF sequence (if found) | Missing if using order upstream
|
| 22 | Source | Source of the hit ORF | Options: sixframe, annotation or both |