[mira_talk] Re: SSAHA2 vector screen
- From: Andy <mirabilis@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 22 Mar 2010 18:46:38 -0700
Apologies for the multiple posts (I'd expected to see my post in my
mira_talk inbox and didn't and so repeated the post).
I'm running mira_3.0.3x1
On Mon, Mar 22, 2010 at 6:07 PM, Cheng-Ruei Lee <cl134@xxxxxxxx> wrote:
> Hi Andy:
>
> I met a similar problem before, and here's the help ticket for it:
> http://sourceforge.net/apps/trac/mira-assembler/ticket/14
> , although I haven't tried the new version Bastien provided. (Sorry about
> that, Bastien.)
>
> Cheng-Ruei Lee
>
> On Mar 22, 2010, at 9:03 PM, Andy wrote:
>
> Hi All,
>
> I'm performing a hybrid assembly of Sanger and Solexa reads. The template
> is 12,000 long cDNA clones that were Sanger end-sequenced and then the cDNA
> inserts were pooled, fragmented, and sequenced to a high depth with Solexa
> 100bp reads. I screened the Solexa reads against the cloning vector
> sequences using SSAHA2 and it seemed to work fine.
>
> But I'm getting the following error messages from mira when I use
> -CL:msvs=yes
> Do I need to set the msvsgs:msvsmfg:msvsmeg parameters?
>
>
> Error! The length of read SOLEXA1_0001:1:74:16647:1029#0/1 (101) does not
> match the length given in the SSAHA2 file (101)
> SSAHA2 line: ALIGNMENT::08 27 SOLEXA1_0001:1:74:16647:1029#0/1 pFLC-I 29 2
> 735 762 C 28 100 101
>
> Error! The length of read SOLEXA1_0001:1:74:17068:1020#0/1 (101) does not
> match the length given in the SSAHA2 file (101)
> SSAHA2 line: ALIGNMENT::50 100 SOLEXA1_0001:1:74:17068:1020#0/1 pCMVSPORT6
> 101 2 811 910 C 100 100 101
>
> Error! The length of read SOLEXA1_0001:1:74:18037:1025#0/1 (101) does not
> match the length given in the SSAHA2 file (101)
> SSAHA2 line: ALIGNMENT::14 32 SOLEXA1_0001:1:74:18037:1025#0/1 pFLC-I 33 2
> 739 770 C 32 100 101
>
> Error! The length of read SOLEXA1_0001:1:74:18037:1025#0/1 (101) does not
> match the length given in the SSAHA2 file (101)
> SSAHA2 line: ALIGNMENT::14 27 SOLEXA1_0001:1:74:18037:1025#0/1 pFLC-I 29 2
> 735 762 C 28 100 101
>
> Error! The length of read SOLEXA1_0001:1:74:18070:1023#0/1 (101) does not
> match the length given in the SSAHA2 file (101)
> SSAHA2 line: ALIGNMENT::50 84 SOLEXA1_0001:1:74:18070:1023#0/1 pCMVSPORT6
> 18 101 797 880 F 84 100 101
>
>
> I'm guessing that SSAHA2 thinks that the reads are 101bp long but mira
> thinks that they're 100bp?
>
>
> I noticed also that mira is doing some filtering of the Solexa reads, what
> do these mean?
> Solexa: Filter out T (hard) SOLEXA1_0001:1:15:12586:2781#0/1
> Solexa: Filter out T (hard) SOLEXA1_0001:1:15:12588:8448#0/1
> Solexa: Filter out (A hard) SOLEXA1_0001:1:15:12595:11576#0/1
> Solexa: Filter out (A hard) SOLEXA1_0001:1:15:12611:16949#0/1
> Solexa: Filter out T (hard) SOLEXA1_0001:1:15:12628:14575#0/1
> Solexa: Filter out (A hard) SOLEXA1_0001:1:15:12634:12867#0/1
>
> Thanks
>
> Andy
>
>
>
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