[mira_talk] Re: Mappging to Reference
- From: Saulo Alves <sauloal@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 15 Jun 2010 13:33:58 +0200
Hello Bastien,
I could successifully perform the alignment. thank you very much.
I still have a question.
How do i interpret this data:
This position would be a insertion This position would
be a deletion
| |
CONTIG : 1
TAACGCCAAAAAAATCAAAAAATCTAAAAAAACTCATTTTTCCGCGCCATTTTTCATTTTTGTTGCGATTTCACTTGCAAAAATGTGCAGG*TAACCGCG
100
READ : 1
------------------------------------------------ATTTTTC*TTTTTGTTGCGATTTCACTTGCAAAAATGTGCAGGCTAACCGCG
100
FASTA : 1
------------------------------------------------ATTTTTC-TTTTTGTTGCGATTTCACTTGCAAAAATGTGCAGGCTAACCGCG
100
what would this
position be?
|
CONTIG : 101
TTTTTTGTGAACTTAGGGCGAAATAAATGAGTCAATCAGTACGCAACAT**GCTTC*TGAATCAGGTATAGCATGATACATTTCATACATAAATCATTAT
200
READ : 101
TTTTTTGTGAACTTAGGGCGAAATAAATGAGTCAATCAGTACGCAACAT**GCTTC*TGAATCAGGTATAGCATGATACATTTCATACATAAATCATTAT
200
FASTA : 101
TTTTTTGTGAACTTAGGGCGAAATAAATGAGTCAATCAGTACGCAACAT--GCTTC-TGAATCAGGTATAGCATGATACATTTCATACATAAATCATTAT
200
Regards
----------------
s.
On Sat, Jun 12, 2010 at 10:01 PM, Bastien Chevreux <bach@xxxxxxxxxxxx>
wrote:
> On Freitag 11 Juni 2010 Saulo Alves wrote:
>> Sorry if i didn't make myself clear.
>> events stands for all the tags mira add's to the sequencing. Gaps,
>> SNPs, repeats.
>>
>> I have tried the AO process but, after placing the gaps, there are
>> still discrepancies.
>> for one chromossome my FASTA reference has 1.462.416 bp. the "PADDED"
>> (w/ gaps) generated sequence has 1.462.514 bp and the "UNPADDED"
>> sequence has 1.462.431 bp.
>> There's this difference (+17) between the original and unpadded which
>> i cant explain neither map back. If i want to know where in the
>> reference sequence a SNP was found, i'm not able with a 17bp
>> discrepancy and, for other chromossome, this difference get's even
>> bigger.
>
> Hmm ... have a look at the TCS file, column 2 & 3 with the padded pos and
> unpadded pos. Would that help?
>
> B.
>
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