SOAPdenovo map question

[Yilong Li]

Dear fellow sequencers,

I am trying to assemble some reads using SOAPdenovo and map the reads to the assembled contigs. In SOAPdenovo, there is a utility SOAPdenovo map, that is supposed to do this. But when I do this, the resulting *readOnContig is empty (leave header line). The output I get from SOAPdenovo-63mer map is:


Version 1.05: released on July 29th, 2010

K = 31
contig len cutoff: 33

there're 1125597 contigs in file: test_fasta_020611, max seq len 5161, min seq len 32, max name len 10
time spent on parse contigs file 11s
8 thread created
time spent on hash reads: 5s
16173369 nodes allocated, 17130136 kmer in reads, 17130136 kmer processed
time spent on De bruijn graph construction: 16s

time spent on mapping long reads: 1s

In file: config.txt, max seq len 85, max name len 256

8 thread created
2250827 edges in graph
0 out of 0 (nan)% reads mapped to contigs
no paired reads found
[LIB] 0, avg_ins 0, reverse 0
time spent on mapping reads: 1s

overall time for alignment: 0m


I am using the same config file and read file for both the assembly and the mapping. So what could be the reason for the failed mapping?


Yilong

[xysheep]

I have faced the same problem with you.
Let's pray for a master-hand to give a solution.

[Yilong Li]

Hi xysheep,

I asked this from SOAPdenovo support back some time ago, and they told me that the map function only works with paired end reads. Hope this helps you!

Yilong