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Hi,
I was searching the forum but couldn't find an answer to my question.
I did some SOAPdenovo assemblies and try to analyze now the outcome. Most results such as k-mer size or contigs are self-explaning but the scaffold file raises more questions.
According to the manual:
" *.scaf
Contigs for each scaffold: contig index (concordant to index in *.contig), approximate start position on scaffold, orientation, contig length, and its links to others contigs."
The output I get:
Which would you now assume is the size, 1043 ??
I was searching the forum but couldn't find an answer to my question.
I did some SOAPdenovo assemblies and try to analyze now the outcome. Most results such as k-mer size or contigs are self-explaning but the scaffold file raises more questions.
According to the manual:
" *.scaf
Contigs for each scaffold: contig index (concordant to index in *.contig), approximate start position on scaffold, orientation, contig length, and its links to others contigs."
The output I get:
Code:
>scaffold1 4 1043 26075626 0 - 149 #DOWN 29730995:10:14 #UP 28841691:1:2468 2545 8047:1:2632 29352643:7:2 29730995 114 + 489 #DOWN 24111965:1:2334 23873283:4:2353 22045038:1 :2577 21124412:1:2504 17741215:1:2406 16945306:1:2668 10685729:1:2337 27409261:7 :83 23816943:7:36 17458719:2:-20 #UP 29182234:2:2296 26511596:2:2377 2625 2134:2:2452 17793434:2:2627 29352643:5:84 26075626:10:14 27409261 637 - 181 #DOWN 21248222:1:2693 19094323:1:2680 15343782:2 :2607 26245018:8:122 24140425:7:60 #UP 28606926:1:2579 26245018:1:2602 2973 0995:7:83 23816943:2:11 17458719:1:69 26245018 891 - 152 #DOWN 27409261:1:2602 24911322:2:2592 19591029:1 :2607 19094323:1:2644 17944793:2:2666 15595171:1:2667 23018463:8:103 15847328:1: 61 15121500:3:82 #UP 28943999:2:2651 18736037:1:2689 14326327:1:2662 2740 9261:8:122 24140425:1:34 15463175:1:106
Which would you now assume is the size, 1043 ??