Re: [wgs-assembler-users] FastqToCA for paired-end reads

[Ole K. T. <o.k...@bi...>]

On 14 May 2012 20:32, Mundy, Michael <Mun...@ma...> wrote:
> I’m using WGS 7.0 and I have two synchronized fastq files with paired-end
> reads.  Based on the documentation at
> http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=FastqToCA,
> I tried this command:
>
> wgs-7.0/Linux-amd64/bin/fastqToCA -libraryname SRR067601.000 -mates
> SRR067601.000_1_pair.fq,SRR067601.000_2_pair.fq
>
> But it returns this error:
>
> ERROR:  Mated reads (-mates) must have am insert size (-insertsize).
>
> The documentation page says that the –insertsize option is optional so I
> thought that was the flag to distinguish between paired-end reads and
> mate-pair reads.  How do I generate a FRG file for paired-end reads?

I guess the documentation is not up to date, so it's not optional to
supply the -insertsize option. Just add -insertsize 300 30, if your
reads are from a 300 bp DNA fragment and are paired end, or do
something like -insertsize 5000 500 -outtie if they are mate pairs
from a 5k library.

Ole

>
> Mike Mundy
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> wgs-assembler-users mailing list
> wgs...@li...
> https://lists.sourceforge.net/lists/listinfo/wgs-assembler-users
>