Hi!
I'm trying to map illumina paired end using MapSplice. I used script named sickle to trim the bad quality tails and the output looks like this:Paired end 1
@TUPAC_0006:1:1:3062:1473#0/1
TGTATGTATCTATAACAATGGCCTTTTGTGTTGTTTTTCTGGGCATGTTGTATGACAATTTCTATTACAGCATATG
+
fYcfffffffgggggfggggdgggfgfggggfggggggggggfgggggggfgggdgegggggggeggcaaf]cefg
@TUPAC_0006:1:1:3623:1474#0/1
TGGGAGGTTAAGAGTAGCATGAAGAACTTAAGATGAGGATAAGAGTCTAAATTTTTAGTTTCAAGGTTTCAATAGA
+
aa^\Sf``cfgg_cfcfcffeeSfff]ffcfffffWfb`dfefeffcfcc[ffffff_fefaaeffdefaacacdg
@TUPAC_0006:1:1:4325:1480#0/1
CAAGAACCGACTAAAACAGACACCATTATGAACTCAATTAATCACCACAACACCC
+
a\^aQ^\a^ZGSNUQd^ZZ[ZZV[Zfce]c]]W^^]]^^]``_``[aa_acaaa_
@TUPAC_0006:1:1:4592:1480#0/1
CGGTTCCTTAAATCAAGTTACATGATGTTGCCTGAATTCAAGTAAACAGGAATGAATAATCCTCCTGTAGGGAAGA
+
haghgghhghgghhhhhhhghechhghh]cfhhhhhhhg]hghhhfhhhhgghghfhchhfdhgghhghhchecfd
@TUPAC_0006:1:1:10714:1476#0/1
GAGCGATACTGATGATGAAATTTTCAAAAATGACTGCCAACTATTTTGAG
+
VDLTMRTTRVPVPV[\_`aTccc[_ccc_a_aRca]aa]a[c[aS^_]]a
@TUPAC_0006:1:1:4409:1497#0/1
GGGAGGGCGATGAGGACTAGGATGATGGCGGGCAGGATAGTTCAGACGGTTTCTATTTCCTGAGCGTCTG
+
fWfafffcfffddddaafaffWff]bdf`fd```ecadWb]cffff_ffdaabb]c_fa]a`Q`^`W\\^
@TUPAC_0006:1:1:6557:1505#0/1
GGCTTATTGTACAGATTATTTTATCACCCAGGTATTAAGCTTAGTACCCATTAGATATCTTTCCCAATCCTCTACC
+
g\_fggggggffffcgggfgggggggfgcfffbffaffffIXZUSgggggggggggfgcgggggggggcfggaefgPaired end 2@TUPAC ...