[mira_talk] info files

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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