Discovar assembly no reference reads(urgent)
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6.9 years ago
lanyuhao1991 ▴ 20

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, a1.fastq, a2.fastq -> 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.

https://groups.google.com/a/broadinstitute.org/forum/?hl=en&fromgroups#!searchin/discovar-user-forum/assemble$20no$20refernce/discovar-user-forum/YcUAxG80-lw/6lo_eKHSAwAJ

Assembly Discovar • 1.4k views
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