unaligned reads

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Hello.

I am having great success with Mosaik...thank you for writing such good 
documentation and for 
the information outputs that accompany each module.

I would like to do a de novo assembly in Velvet of the unaligned reads 
generated by Mosaik.  But 
I noticed that Mosaik does not retain the order of the paired reads when 
dumping unaligned 
reads to the fastq file.  Do you (or does anyone reading this) have a script to 
re-organize the 
unaligned reads file in the required order for Velvet?  (i.e., Read 1 of a pair 
is immediately 
followed by Read 2, then Read 1 and Read 2 of another pair, etc.)  I am willing 
to toss the 
"orphaned" reads from the unaligned reads file.

Thank you,
Laura Williams

Original issue reported on code.google.com by laura.w...@gmail.com on 4 Mar 2010 at 3:31

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Original comment by WanPing....@gmail.com on 27 Oct 2010 at 6:54

• Changed state: Accepted

[GoogleCodeExporter]

To follow up with this (in case anyone runs across this comment and has a 
similar problem), the most recent version of Velvet now accepts "unordered" bam 
files that include both paired end and single end reads.  According to the 
developer, it will use the paired end information.  

Original comment by laura.w...@gmail.com on 15 Feb 2011 at 4:49

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Yes, MOSAIK2, the one we are still working on, will feature this.

Original comment by WanPing....@gmail.com on 15 Feb 2011 at 10:11