Improving/extending exons rather than introducing a new exon
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#2 Improving/extending exons rather than introducing a new exon
I think I have a nice testcase for you. SIBsim4 does not initiate an alignment in this case since position 1 due to mismatch at position 3. This can be avoided by "-r 2". However, that does not help to get extended alignment on the 3'-end where ... I hope is just a crappy sequence and real junk or vector contamination etc.
>149234350 Mus musculus chromosome 1 genomic contig, strain C57BL/6J.; LEN=70622195
>CB573166 AGENCOURT_12799049 NIH_MGC_165 Mus musculus cDNA clone IMAGE:30279251 5', mRNA sequence.; LEN=756
1766879-1766916 (4-41) 100% -> (GT/AG) 24
1772478-1772592 (42-156) 100% -> (GT/AG) 24
1773817-1773951 (157-291) 100% -> (GT/AG) 24
1777250-1777354 (292-396) 100% -> (GT/AG) 24
1778747-1778899 (397-549) 100% -> (GT/AG) 24
1778994-1779130 (550-694) 91%
[cut]
$ SIBsim4 -A 4 -r 2 chromosome_hits/chr_1_NT_078297.dna /tmp/a.dna
>149234350 Mus musculus chromosome 1 genomic contig, strain C57BL/6J.; LEN=70622195
>CB573166 AGENCOURT_12799049 NIH_MGC_165 Mus musculus cDNA clone IMAGE:30279251 5', mRNA sequence.; LEN=756
1766876-1766916 (1-41) 97% -> (GT/AG) 24
1772478-1772592 (42-156) 100% -> (GT/AG) 24
1773817-1773951 (157-291) 100% -> (GT/AG) 24
1777250-1777354 (292-396) 100% -> (GT/AG) 24
1778747-1778899 (397-549) 100% -> (GT/AG) 24
1778994-1779066 (550-622) 100% ==
38009609-38009629 (637-658) 86% -> (GC/AG) 17
38085474-38085493 (659-678) 85%
In general, I would prefer a way to specify that I rather want _isolated_ mismatches in the alignment over newly introduced "exons" too far away, and definitely not with unmatched regions (shown with those ==).
Have you tried tweaking -C, -K, -W, and -X. Since you increase the match reward, I'd suggest increasing -K too, to avoid picking up small, uninteresting matches.