Re: [AMOS-help] Help needed! Conversion from afg to SAM for paired-end reads

[Florent A. <flo...@gm...>]

Hi Makis,

Please keep your messages on the list. I don't know if or when I'll have 
time to look at this, but other developers may be in a better position 
to help.
Best,

Florent


On 12/10/11 22:55, Makis Ladoukakis wrote:
> Hello Florent,
>
> Thank you for your immediate reply. I have uploaded the .afg file 
> (splitted this file into two volumes as it was too big to upload) and 
> the resulting SAM and fasta files here:
> https://skydrive.live.com/redir.aspx?cid=965b66d12e5d1c81&resid=965B66D12E5D1C81!264
>
> I have installed the latest version of AMOS (3.0.1) and the commands i 
> used were the following:
>
> bank-transact -m velvet_asm.afg -b velvet_asm.bnk -c
> bank2fasta -i -b velvet_asm.bnk>  velvet_asm.fa
> bank2contig -i -s velvet_asm.bnk>  velvet_asm.sam
>
> About the SAM file, i contacted one of the developers of Tablet (http://bioinf.scri.ac.uk/tablet/) Mr Iain Milne asking why his software
> whereas supporting viewing paired end reads in SAM files couldn't display mine. This is the response i got:
>
> "That sam file does not contain flags that mark any of the reads as paired-end, therefore I'd assume that the amos script you used to
> convert from AFG just doesn't support doing that.
>
> Iain"
>
>
> Hawkeye doesn't support the import of SAM files so i cannot verify 
> whether Mr Iain's claim is true in another viewer except Tablet
>
> Thank you in advance,
> Makis
>
>
> ------------------------------------------------------------------------
> Date: Wed, 12 Oct 2011 21:05:17 +1000
> From: flo...@gm...
> To: lad...@ce...
> CC: amo...@li...; amo...@li...
> Subject: Re: [AMOS-help] Help needed! Conversion from afg to SAM for 
> paired-end reads
>
> Hi Makis,
>
> Could you provide a small dataset to reproduce the problem? Also, what 
> commands did you run precisely and do you have the latest version of 
> AMOS? How does one know if a SAM file has paired-end information in it 
> or not?
> Best,
>
> Florent
>
>
>
> On 12/10/11 20:18, Makis Ladoukakis wrote:
>
>     Dear AMOS developers,
>
>     I am using AMOS converter Bank2contig to convert .afg files
>     containing paired-end data to SAM files to use in the Tablet
>     viewer (as shown in
>     http://sourceforge.net/apps/mediawiki/amos/index.php?title=Bank2contig
>     ). Nevertheless after the conversion the resulting SAM file
>     doesn't contain flags that mark any of the reads as paired-end.
>     When I use the Hawkeye viewer and insert the bank file from which
>     the SAM file results my reads are recognised as paired-end.
>     Doesn't the converter support conversion of paired-end data from
>     bank to SAM?
>
>     Thank you,
>     Makis
>
>
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