[mira_talk] Re: Mappging to Reference
- From: Saulo Alves <sauloal@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 11 Jul 2010 13:22:22 +0200
Contig is the unpadded contig
read is the padded contig
fasta is the reference fasta.
I have solved this problem already.
As I have stated, i wanted to be able to align both sequences and "events"
so that i could align it with the data about the sequence.
In this example, i have the reference sequence aligned with the gapped
contig and all SNPs, gaps, insertions, deletions, regions of low quality
(called events - S stands for SMTP) and ND (regions without reads) plus
mapped genes and microarrays probes.
Now i can try to correlate modifications of the dna with microarray profiles
and disruptions of important genes. Well, might be a long shot.
Regards,
SNP
||
INSERTION SNP INSERTION
|| |
| |
REFERENCE: 1
A--------------------------------------------------TTC-ACATCTCTTTGTTGCGCGATGTGATTGGCTTCTTC-CCCCTAAGG
100
CONTIG : 1
AGCACATCGACAATTTTTGGGGGTCATACACTGATCTCCTGGCTTTAGATCGCCAACATCTCTTTGTTGCGCGATGTGATTGTCTTCTTCACCGCGAAGG
100
SNP : 1
s--------------------------------------------------ss-----------------------------s----------s-s----
100 SNPS
INS : 1
-iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii---i-----------------------------------i---------
100 INSERTIONS
GAP : 1
----------------------------------------------------------------------------------------------------
100 GAPS
DEL : 1
----------------------------------------------------------------------------------------------------
100 DELETIONS
EVENT : 1
M--------------------------------------------------SSS-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-SSSSSSSSS
100 LOW QUALITY
ND : 1
----------------------------------------------------------------------------------------------------
100 LOW COV./NO DATA
GENE : 1
-------------------------------------------------------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCC
100 GENE
MICRO : 1
----------------------------------------------------------------------------------------------------
100 MICROARRAY
SNP DELETION
| | |
REFERENCE : 101
CGCCGCCAGGGGGCCGGCCGGGCACACTGGCGTTTTTTTCACAACCTCCTGGCTGGTCAGCATCTCTGCGATCCTTGTGATAAAAGAGGCTACGTATCGT
200
CONTIG : 101
CGCCGCCAGGGGTCTGGCCGGTCACACTGG*GTGAGTTTCACAACCTCCTGTCTGGTCAGCATCTCTGCGATCCTTGTGATAAAAGAGGCTACGTATCGT
200
SNP : 101
------------s-s------s-----------sss---------------s------------------------------------------------
200
INS : 101
----------------------------------------------------------------------------------------------------
200
GAP : 101
----------------------------------------------------------------------------------------------------
200
DEL : 101
------------------------------d---------------------------------------------------------------------
200
EVENT : 101
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
200 LOW QUALITY
ND : 101
----------------------------------------------------------------------------------------------------
200
GENE : 101
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
200 GENE
MICRO : 101
----------------------------------------------------------------------------------------------------
200
GAP
|
REFERENCE: 5801
GGAGGTCATTCTTGAGCGGGGGGAACTGGATGTCCCTCCATGAGTTGACAAGGTCGAGTTTGGGGACTGCGTGGGACA-TTGTGTGT-TATG-GTATGTA
5900
CONTIG : 5801
GGAGGTCATTCTTGAGCGGGGGGAACTGGATGTCCCTCCATGAGTTGACAAGGTCGAGTTTGGGGACTGCGTGGGACA*TTGTGTGT*TATG*GTATGTA
5900
SNP : 5801
----------------------------------------------------------------------------------------------------
5900
INS : 5801
----------------------------------------------------------------------------------------------------
5900
GAP : 5801
------------------------------------------------------------------------------g--------g----g-------
5900
DEL : 5801
----------------------------------------------------------------------------------------------------
5900
EVENT : 5801
----------------------------------------------------------------------------------------------------
5900
ND : 5801
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx-xxxxxxxx-------------
5900 LOW QUAl
GENE : 5801
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCC-CCCC-CCCCCCC
5900 GENE
MICRO : 5801
----------------------------------------------------------------------------------------------------
5900
----------------
s.
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