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