dear Biocers*

I have just received data from solexa facility.

I tried the packages ShortRead and Rolexa, but it seems to me they require a
specific file organization with 3 main folder as the imput.

instead I have 2 type of file: the first looks like that

HWI-EAS373    1    2    1    1    1    0    1
NAGCCAGCTTACCTCCCGGTGGTGGGTCGGTGGTCCCTGGGCAGGGGTCTCCCGATCCCGGACGAGCCCCCCAAT
DGPRTTTTRRRTTTRTRTTTTTQPPTSUQPQPTSPSSSSBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
NM                                            Y
HWI-EAS373    1    2    1    2    2    0    1
NATCTGTTCTTGGCCCTGAGCCGGGGCAGGAACTGCTTACCACAGATATCCTGTTTGGCCCATATTCAGCTGTTC
DKWUWUUWVUSWUWWWWUUUWWUWVVWSSSWVWSWUWVWWSSTQUVWWVWUWWQWVWWWQWSRKPWVWVWVUQWW
NM                                            Y
HWI-EAS373    1    2    1    3    3    0    1
NACCTTACACAGTCCTGCTGACCACCCCCACCGCCCTCAAAGTAGACGGCATCGCAGCTTGGATACACGCCGCCC
DLRPPNSPRTTSPRRFSTSTSRRTRPRPSNSPRRNQRNTTRPKTSNRPPPSTTSRTBBBBBBBBBBBBBBBBBBB
NM                                            N
HWI-EAS373    1    2    1    4    4    0    1
NAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTG
DOZXZUZZVZZZOXZUZWWUYXXXRZWMMMGWYNYXXTXXXXVBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
NM                                            Y
HWI-EAS373    1    2    1    5    5    0    1
NATAGAATGTCATGGCACTGTTCAGAATGGCATACAACAACGGCCAGGTCTGCAGCCACATCAGGGCAAACACAT
DMWRWSVXYRSNPXXWSPXXXYXUXXXYXTGTUXXSRWUWWYXYWXXYUXYXUXWWVXWVVVRUYXTTTVXXWTW
NM                                            Y
HWI-EAS373    1    2    1    6    6    0    1
NAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAAC
DKUUYXUXXXXXURYXUXYXXXXYXXYUXWTTXXWVXXUXYYYUYYWSWXVSVXUXWPVWXVVVVVTNTWVVSVB
NM                                            Y
HWI-EAS373    1    2    1    7    7    0    1
NCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAA
DMWYYYUWSWWTYWYWWUWUWWYWYVVWWWWUWWWTVVYYWWWYTUWUWTYUVXTTUSSWVTWWURWUWNSUWQP
NM                                            Y
HWI-EAS373    1    2    1    8    8    0    1
NAGCGTGGGTCCCACTGTATCATTGGGGCACTGGTGCCAGGTTGAAAGTCCACCCGTCACGACCTTCTACACATG
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
NM                                            N
HWI-EAS373    1    2    1    9    9    0    1
NAAACCTCTNACACATGCAGCTCCCGGAGACGGTCACAGCTTGTCTGTAAGCGGATGCCGGGAGCAGACAAGCCC
DKTTSTTTMDNTTSSSTTTTSTTTRSUTRTTTTRSRSNPRRSSPSSTRBBBBBBBBBBBBBBBBBBBBBBBBBBB
NM                                            N
HWI-EAS373    1    2    1    10    10    0    1
NGGTTCTCTAGAAACTGCTGAGGGCTGGACCGCATCTGGGGACCATCTGTTCTTGGCCCTGAGCCGGGGCAGGAA
DKRRTTRSSSSTNOSSNTQKQPNPUTMPPRSSOSSPRRRRSRSRSTBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
NM


the second like this one

HWI-EAS373    1    2    1    1    1    0    1
NAGCCAGCTTACCTCCCGGTGGTGGGTCGGTGGTCCCTGGGCAGGGGTCTCCCGATCCCGGACGAGCCCCCCAAT
DGPRTTTTRRRTTTRTRTTTTTQPPTSUQPQPTSPSSSSBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
NM                                            Y
HWI-EAS373    1    2    1    2    2    0    1
NATCTGTTCTTGGCCCTGAGCCGGGGCAGGAACTGCTTACCACAGATATCCTGTTTGGCCCATATTCAGCTGTTC
DKWUWUUWVUSWUWWWWUUUWWUWVVWSSSWVWSWUWVWWSSTQUVWWVWUWWQWVWWWQWSRKPWVWVWVUQWW
NM                                            Y
HWI-EAS373    1    2    1    3    3    0    1
NACCTTACACAGTCCTGCTGACCACCCCCACCGCCCTCAAAGTAGACGGCATCGCAGCTTGGATACACGCCGCCC
DLRPPNSPRTTSPRRFSTSTSRRTRPRPSNSPRRNQRNTTRPKTSNRPPPSTTSRTBBBBBBBBBBBBBBBBBBB
NM                                            N
HWI-EAS373    1    2    1    4    4    0    1
NAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTG
DOZXZUZZVZZZOXZUZWWUYXXXRZWMMMGWYNYXXTXXXXVBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
NM                                            Y
HWI-EAS373    1    2    1    5    5    0    1
NATAGAATGTCATGGCACTGTTCAGAATGGCATACAACAACGGCCAGGTCTGCAGCCACATCAGGGCAAACACAT
DMWRWSVXYRSNPXXWSPXXXYXUXXXYXTGTUXXSRWUWWYXYWXXYUXYXUXWWVXWVVVRUYXTTTVXXWTW
NM                                            Y
HWI-EAS373    1    2    1    6    6    0    1
NAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAAC
DKUUYXUXXXXXURYXUXYXXXXYXXYUXWTTXXWVXXUXYYYUYYWSWXVSVXUXWPVWXVVVVVTNTWVVSVB
NM                                            Y
HWI-EAS373    1    2    1    7    7    0    1
NCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAA
DMWYYYUWSWWTYWYWWUWUWWYWYVVWWWWUWWWTVVYYWWWYTUWUWTYUVXTTUSSWVTWWURWUWNSUWQP
NM                                            Y
HWI-EAS373    1    2    1    8    8    0    1
NAGCGTGGGTCCCACTGTATCATTGGGGCACTGGTGCCAGGTTGAAAGTCCACCCGTCACGACCTTCTACACATG
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
NM                                            N
HWI-EAS373    1    2    1    9    9    0    1
NAAACCTCTNACACATGCAGCTCCCGGAGACGGTCACAGCTTGTCTGTAAGCGGATGCCGGGAGCAGACAAGCCC
DKTTSTTTMDNTTSSSTTTTSTTTRSUTRTTTTRSRSNPRRSSPSSTRBBBBBBBBBBBBBBBBBBBBBBBBBBB
NM                                            N
HWI-EAS373    1    2    1    10    10    0    1
NGGTTCTCTAGAAACTGCTGAGGGCTGGACCGCATCTGGGGACCATCTGTTCTTGGCCCTGAGCCGGGGCAGGAA
DKRRTTRSSSSTNOSSNTQKQPNPUTMPPRSSOSSPRRRRSRSRSTBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
NM


can i import them in the pipeline of analyses provided by bioconductor?
which package is the most suitable??
*

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