A small problem with our data

''We must free ourselves of the hope that the sea will ever rest. We must learn to sail in high winds, Onasis''

Oliver today realized that we had a problem with the data that Lars gave us. So discussed a bit and he sent an email for clarification.

''I was just looking at making my config file for running SOAPdenovo and was noticing that it can only take interleaved paired reads in one file if it is a fasta file and not in a fastq for some reason. So to solve this I was looking at converting the fastq to fasta so soap could take it or to separate the paired reads into separate files. However, as I started to examine the file it didn’t seem like the reads came paired like you explained in the email.

The first 20 lines of the unzipped file looks like this:

@HWI_ST139:1:1:3619:1964#0/1 1 AAANTTCGAGTTCTCTGATTTTGAATTTCAGAGGATGAGTCTTTGCTGGAAGTTGAGTTATCCTATGAGTGTTTAN +HWI_ST139:1:1:3619:1964#0/1 1 ]VPBVP_IVLb\b\baacaa_c_dccceee``dd]]ddcdddcc^aLUSVV^U[___bbbbbb```^BBBBBB @HWI_ST139:1:1:4376:1963#0/1 1 TGGNCGCACACATTTGATTTTTCCATGTTGGCATGCATTCATGATGAGTCGCAACTACCATTAGGTAAAAGAACTN +HWI_ST139:1:1:4376:1963#0/1 1 VV\B\\Z^[c\cccc`ccYccc`\c^ccc^cccacccca`bbYTcTc^a]a```^`YYYbb_Yb^bbYbaBBBBB @HWI_ST139:1:1:5347:1963#0/1 1 GGANTGTCCTTGCAATCTTCCTTGTATATCTTTTTATCCCCTTTGATTGTTTCTTCATAAATTTTTGGATTTGTTN +HWI_ST139:1:1:5347:1963#0/1 1 `\B\babbbffffdfefefeeeceefeffffffffbfffffcffdffffdfdffeffdaceffeeecce```]`B @HWI_ST139:1:1:6144:1963#0/1 1 GTTNCACAGCTCCTTGAAGTTTTTCTTAGCAATTCAGTTCTCCCTTCAATCCGTTTTAAAATTCGAAAGCATCCAN +HWI_ST139:1:1:6144:1963#0/1 1 X[B]ababbfffffeaccefddfeffffecffffecdeeffffffeffeffffffcfcfcfffceeee`aaZ]aB @HWI_ST139:1:1:7188:1963#0/1 1 CACNGTTACCGGGGCCCAAAATTAGGGTTTTGAAAAAGTGAGAGTTTTCAGCTATCTATCACCATAGAAAGTTGCN +HWI_ST139:1:1:7188:1963#0/1 1 _`ZB`b_b__ededeeceeeeYeceeeTeceeeeeeeaTc`bbb\addddeee`eeeeYYddddaeecedZY]aaB

There doesn’t seem to be any reads that end with 2 or are they in a different part of the file?''