[mira_talk] info files
- From: "Shai Uliel" <shai@xxxxxxxxxxxxxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Tue, 21 Apr 2009 16:07:47 +0200
Hi Bastien.
I run MIRA2
and the results look very good.
I thing that I found some bugs or I doesn't understand MIRA2 files.
1)
One cluster From my clusters:
>lcl|reads_lrc19975 No definition line found
TGTACAATCGSCYGGGGGAGAGTAAAAATACATGAGGTGATTTCAAGAGGATGGGTGCTATCAAGAGTAAAG
TGCCATTG
AGCATATTCAAGCATGTGTATTATGGCACCCTTTTTCTTTACCTGACTTCATTTCAGATACACAACCAAGAC
AGCCATCA
GAGGCATGTAAAGATGCTTTTGTAAACCCAGCATTACTGAGATACCGGGTCATGCTAATTTTTAC
From file info/reads_info_consensustaglist.txt
reads_lrc19975 10 10 10 10 IUPc Strain'default': S
reads_lrc19975 12 12 12 12 IUPc Strain 'default':
Y
12345678901234567890
TGTACAATCGSCYGGGGGAG
It look like the location need to be 11 and 13. And not 10 12 (1 bp
shift)
2)
My fasta file has ~1M reads 454 est but the seq are in one line like
this:
>1
AGAGAGAGAGGGGGGGGGGGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAACCTTCTCTCTCTCTTC
>2
.....
From file info/reads_info_readtaglist.txt ......
reads_lrc1 684 727 659 700 MRMr EHZ8CPV01CCJDE
52 95
.....
reads_lrc1 671 688 649 662 MRMr EHZ8CPV01A5HAK
115 132
......
reads_lrc214 237 252 227 241 MRMr EPE3D2102GTQVD
282 297
......
reads_lrc253 313 483 292 458 MRMr EPE3D2102G3MS6
181 351
.....
The number from reaTo from file reads_info_readtaglist.txt are more
than the length of seq!!!!
this are my est:
>EHZ8CPV01CCJDE len=90bp
AAGCAGTGGTATCAACGCAGAGTGCCCATTACAGCCGGGGGGAAGGAGCCCAGCATGAGAATCGATCGCCCT
CGGCGTTCGAATTGTAGT
>EHZ8CPV01A5HAK len=120bp
AAGCAGTGGTATCAACGCAGAGTAGCCATTACGGCCGGGGTTTAGGCATATCAATAAGCGGAGGAAAAGAAA
CTAACAAGGATTCCCCTA
GTAACGGCGAGCGAACCGGGAAGAGCCCAG
>EPE3D2102GTQVD len=290bp
CGGCCTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTAGAGGCAAATTTTT
TTTATTTA
GCATTCTTAGTACAAGACACCATATAGGTGTAAGATTTGTATCAAGGCACTATAACAAGTTGTGGCACGTTA
TCAACCAT
ATTTATTTAGGATAGGATGACAGGGGACTTTCTTCTGATCCGGTGTCTGACAGCTGCTTCCCTTAAGCCTTT
TATATCTT
CACCTTTTCAGCAGTGGTCATGATCGCTCTCACTCTCGCTGCTGCTGCTG
>EPE3D2102G3MS6 len=340bp
CGGCCTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTNTTTTTTTTTTTTTTTTAAGGAAAAG
CACGGTCA
TACGCAAATGTAATGTCAAATTAGGCCGGCCACTATTACACAAACCCATTTACCCCAGGCAACATCATTGTC
TTTGCCCT
TTTGAATCCGACTAAAAAAGAACAAACTACGATCCTGCCTATATCATATCTGAAAAGTCCTAGAAGTCCAAC
TTAACAAG
CAAAGAACAAAAGAAACACCACCGAAACACCACCGCCAAGATTCAATTTCTTCCTCCCATTTCAGGAGAAAC
AGCCTAGG
CACGCTCGCCCCGGATTCCG
Regards,
Shai
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