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the meaning of *.link and *.newContigIndex from SOAPdenovo1.5
Hi everyone, I want to ask four questions.
The first one is that when I run SOAPdenovo2, it seems to get wrong and output "100000th" . For example,
10000th
20000th
30000th
……
Never stop!
At end, I changed to SOAPdenovo1.5. It run successfully.
The second one is that I want to know the meaning of *.links and *.newContigIndex. For example, the *.links have five columns and the *newContigIndex have three columns. I list four columns below separately.
*.links:
2547 21349 1325 8 1687
4180 9193 1588 1 1687
4180 9193 1588 1 1687
5093 17288 1516 1 1687
*.newContigIndex
1 1 2
2 2 0
3 3 2
4 4 0
The three one is the meaning of the last column in *.updated.edge. I feel that maybe it is about coverage and have conections with the coverage in *.contig.
*.contig
>5 length 32 cvg_35.0_tip_o
>7 length 32 cvg_65.0_tip_0
……
*.updated.edge
>length 0, kmers, kmers, 1, 170
>length 0, kmers, kmers, -1, 170
>length 0, kmers, kmers, 1, 10
>length 0, kmers, kmers, -1, 10
>length 1, kmers, kmers, 1, 350
>length 1, kmers, kmers, -1, 350
The four one is that I found there are many short contigs in my *.contig. I want to assemble paired-end reads in metagenomics. I hope you can give me some suggestions.
I look forward from your. Thank your very much.
your sincerely,
Yue Xu
The first one is that when I run SOAPdenovo2, it seems to get wrong and output "100000th" . For example,
10000th
20000th
30000th
……
Never stop!
At end, I changed to SOAPdenovo1.5. It run successfully.
The second one is that I want to know the meaning of *.links and *.newContigIndex. For example, the *.links have five columns and the *newContigIndex have three columns. I list four columns below separately.
*.links:
2547 21349 1325 8 1687
4180 9193 1588 1 1687
4180 9193 1588 1 1687
5093 17288 1516 1 1687
*.newContigIndex
1 1 2
2 2 0
3 3 2
4 4 0
The three one is the meaning of the last column in *.updated.edge. I feel that maybe it is about coverage and have conections with the coverage in *.contig.
*.contig
>5 length 32 cvg_35.0_tip_o
>7 length 32 cvg_65.0_tip_0
……
*.updated.edge
>length 0, kmers, kmers, 1, 170
>length 0, kmers, kmers, -1, 170
>length 0, kmers, kmers, 1, 10
>length 0, kmers, kmers, -1, 10
>length 1, kmers, kmers, 1, 350
>length 1, kmers, kmers, -1, 350
The four one is that I found there are many short contigs in my *.contig. I want to assemble paired-end reads in metagenomics. I hope you can give me some suggestions.
I look forward from your. Thank your very much.
your sincerely,
Yue Xu