Hi all, I need your help.
I have reads (fastq,pair-end) that have no reference genome. I want to use Discovar to assembly(no reference). I use the following step:
1. First, I convert pair-end fastq files to bam file. (for example,
a.bam). The bam has no region information because I do not have reference genome. BAM file is about 21Gb
2. Second, I use Discovar. When I use this command:
Discovar READS=M2_AACG_L002_R.bam OUT_HEAD=assembly REGIONS=all TMP=tmp
the result is:
Using no REGIONS restriction when the BAM files total more than 10737418240 bytes, which is not officially supported at this time. Sorry, Discovar cannot proceed.
If I change the REGIONS to 0
Discovar READS=M2_AACG_L002_R.bam OUT_HEAD=assembly REGIONS=0 TMP=tmp
The result is :
```There appears to be an incompatibility between your READS and REGIONS arguments. Specifically, the region 0 refers to reference record 0, which is not declared in the header for bam file
M2_AACG_L002_R.bam. Sorry, Discovar cannot proceed. ```
Do you know how can I solve this question?
And how can I declared the reference record in the header for bam file?
Thanks a lot, I need your help.
There are more information in google group