[mira_talk] SSAHA2 vector screen
- From: Andy <mirabilis@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 22 Mar 2010 18:03:54 -0700
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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