[mira_talk] Re: SSAHA2 vector screen
- From: Cheng-Ruei Lee <cl134@xxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 22 Mar 2010 21:07:25 -0400
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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