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\_fggggggffffcgggfgggggggfgcfffbffaffffIXZUSgggggggggggfgcgggggggggcfggaefg
Paired end 2
@TUPAC_0006:1:1:3062:1473#0/2
CNNTNCCTTANNTNTTCNGGANTTATACATACAAGAAAGTTTNCCNNNACCCTATCTTATCCCAATTGTCCCATAT
+
NBBYBJZXSMBBVBW[QBIGIB]Q]LUY]YaKaa^affcf]_BK\BBBXVUWSY[h_hhfhgfchfch]hhfhhhg
@TUPAC_0006:1:1:3623:1474#0/2
TNNANTGCCCNNGNTTTNCTTNTTCCTATGGTTACCCTTTCTNCANNNTGTCCTTTTTGAAAGTTTTGAATATATC
+
[BBVBTGVYTBBSBJWTB][^BLV[__Z_WWaY\\fafd[Q[BVVBBB[SVRT^Vcfffdcdcdfafffdafffah
@TUPAC_0006:1:1:4325:1480#0/2
TNNTNTTCATNNTNCACNTTTNGAAATCTTGCTTGGCATCTTNTTNNNCTGCAAAATAAGGTGATGATTGTACCTA
+
UBB]BTTSVYBBGBTVQBTNSBNUVYY^YHY^a\Tc\dYdRTBWTBBBSZVUNOWaR^V\ZM\TT^Ya^ZaRa[dB
@TUPAC_0006:1:1:4592:1480#0/2
TNNTNTATTANNANTTTNTTTNAATTCTTTTTGTGATTGTTGNACNNNTCGACTGTATTCTGTGCTCTTCCCTACA
+
VBBYB[WX[IBBVBTUYB[OKB[]XSYXWTf]_c`eSeedWTBSWBBBTWZ[X^^hhhhghehhhhhhhfhfgche
@TUPAC_0006:1:1:10714:1476#0/2
TNNGNTCTTNNTNNCTAAANGTACNTCTTAAATCATTTCCTGTTTNNTAAGCTCAGTTCCGCTTGGTGCGTCAAGC
+
VBBSBQTT[BBVBBRVIGNBQPVKBYVWRJaSbL^_]_ZKGHWQPBB]QQWGFSQa^L^cac]^^_`dddZY^[Y\
@TUPAC_0006:1:1:4409:1497#0/2
TNNCNCATAANNANTTTNCTTNTCTTCTTCCTAGTCCTGGAGNCCNNNTTCCTAACACTCACAACAAAACTAACTA
+
UBBVBNTSRRBBUBTSMBVSVBXNTNWTTNa_Z^\`R__ZISB[]BBB[Z^Z^^^fdffddaaffhhchXafdfch
@TUPAC_0006:1:1:6557:1505#0/2
CNNANTTATANNGNTACNTTAACANCACATGCTGGACCCGTTNCGNNNATGGAGGATGGGAGGGGGTAGAGGATTG
+
SBBWB[VSXWBBVBF[KB]VHWSTB_a``]IYZN]fdffa^PBVZBBBQWZ^I]V`bddddhhhh_\bdQaa[[_f
As you can see, both files has the trimmed paired reads in the same order.
When I try to map this reads with MapSplice, the pipeline stops the " Aligning spliced reads" step. Here MapSplice normaly call to a script named "mapsplicesegments" that use an entire core, but when I run MapSplice using this data "mapsplicesegments" is not called:
[Mon Apr 9 18:16:03 2012] Beginning Mapsplice run (v1.15.2)
-----------------------------------------------
bin directory: [/home/geparada/MapSplice_1.15.2/bin/]
[Mon Apr 9 18:16:03 2012] Checking for chromosomes files or directory
[Mon Apr 9 18:16:03 2012] Checking for chromosomes files or directory passed
[Mon Apr 9 18:16:03 2012] Checking for Bowtie index files
[Mon Apr 9 18:16:03 2012] check reads format
[Mon Apr 9 18:16:03 2012] merge paired end reads remove short
[Mon Apr 9 18:16:04 2012] Converting bowtie mapped to SAM format
[Mon Apr 9 18:16:04 2012] divide reads
[Mon Apr 9 18:16:08 2012] Mapping reads against bowtie_index_GM12878_Joel_Rozowsky_paternal with Bowtie
[Mon Apr 9 18:17:23 2012] sort segmentbwt
[Mon Apr 9 18:17:29 2012] reads all chromo sizes
[Mon Apr 9 18:17:33 2012] mapsplice_search
[Mon Apr 9 18:17:52 2012] Aligning spliced reads
MapSplice have only problems with the trimmed paired, because the same reads before the trim can be mapped with MapSplice without any problems.
Anyone got an idea what may be wrong here ?
Thanks for your time!