Mapping Trimmed Paired End Reads With Mapsplice

Question

[Geparada]

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 "mapsplice_segments" that use an entire core, but when I run MapSplice using this data "mapsplice_segments" 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!

Answer 1

[Geparada]

MapSplice 1.15.2 doesn't support paired end reads with different length!!!!

The authors of MapSplice said to me that only the beta MapSplice 2.0 can run this kind of reads. So I tried and it works perfect (and much faster than previous version) !!!

[Nicolas Rosewick]

where did you download Mapsplice 2.0 ?

[Geparada]

It isn't released yet, so you have to send a mail to the authors ( [e-mail] ) and ask for it!

[yangzou306]

Hello Geparada ；

I am learning mapsplice now, and I have seen the manual,but it still can't work well, can you give me your code (pairend).

Thank you !

[Geparada]

Are you using the 1.15.2 or 2.0 version? email me at [e-mail]