Re: [Bio-bwa-help] bwa run error! First time user...

[Matt E. <matted@MIT.EDU>]

Here the database is the reference genome that you want to align your reads
against.  If you're interested in aligning against plasmodium, you would
probably download the genome version you want as a FASTA file from NCBI or
another resource.  In other situations you might include other species or
strains; it all depends on what you're trying to do in your analysis.

Here is one tutorial for using bwa which may complement the manual (others
on the list might suggest other/better ones):
http://icb.med.cornell.edu/wiki/index.php/Elementolab/BWA_tutorial.

Matt

On Wed, Jun 20, 2012 at 4:12 PM, Aragam, Nash Ramarao <
nas...@me...> wrote:

>  Matt,****
>
> ** **
>
> Ah….okay…will do it first. But then, I’m not sure I understand the
> “database” context here? Especially if it takes a couple of hours, are we
> talking about giving this program a whole database of reference seqs? If
> so, can you throw a little more light upon how one could go about
> constructing a reference database for microbial genome like P. falciparum
> or do we just use some canned database like the one available from NCBI?
> Perhaps the latter?****
>
> ** **
>
> Thanks much for my email education….;-) but then please point me to some
> fundamental reading before going about using these new tools. ****
>
> ** **
>
> Best, Nash****
>
> ** **
>
> ** **
>
> *From:* Matt Edwards [mailto:ma...@mi...]
> *Sent:* Wednesday, June 20, 2012 4:03 PM
> *To:* Aragam, Nash Ramarao
> *Cc:* bio...@li...
> *Subject:* Re: [Bio-bwa-help] bwa run error! First time user...****
>
> ** **
>
> Have you indexed your reference genome?****
>
> ** **
>
> See the manual at http://bio-bwa.sourceforge.net/bwa.shtml:****
>
> ** **
>
> "For both algorithms, the database file in the FASTA format must be first
> indexed with the *‘index’* command, which typically takes a few hours."***
> *
>
> ** **
>
> Matt****
>
> ** **
>
> On Wed, Jun 20, 2012 at 3:40 PM, Aragam, Nash Ramarao <
> nas...@me...> wrote:****
>
> Hello,****
>
>  ****
>
> I ran my first bwa sw with a PacBio sample and got this file read error –
> ****
>
>  ****
>
> [aragam@kure-login1 aragam]$ bwa bwasw Var2CSA-3d7-RefSequence.fasta
> 008_Mix_2.5kb_B01_1_0124_1.ccs.fasta >008_MixAligned.sam &****
>
> [1] 10712****
>
> [aragam@kure-login1 aragam]$ [bwt_restore_bwt] fail to open file
> 'Var2CSA-3d7-RefSequence.fasta.bwt'. Abort!****
>
>  ****
>
> So my assumptions about the reference and the read files are perhaps
> wrong. Could someone correct me and tell me what the syntax of the command
> is and what input parameters the command is expecting including the format
> of the files?****
>
>  ****
>
> TiA, Nash****
>
>  ****
>
> Nash Aragam MTech, MScCS, DrPH****
>
> Postdoctoral Research Associate****
>
> Dr. Juliano’s Lab; Division of Infectious Diseases****
>
> School of Medicine****
>
> Michael Hooker Research Building, #3206****
>
> University of North Carolina****
>
> Chapel Hill, NC 27599 , USA****
>
>  ****
>
>
>
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