[mira_talk] How do you call your ABI traces?
- From: John Nash <john.he.nash@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 16 Sep 2011 17:23:36 -0400
I recently have been wondering about my ABI tracefiles that I get back from the
sequencing centre. I'm trying to find out why MIRA ditched the reads as debris.
They were gap closure PCR sequences from genome template (I used the
phred-generated ones in my assembly).
IBack in the '90s, I used to use pregap to call my traces because I used the
Staden package for everything. When I sequenced my first genome in the old
pre-NGS days, my bioinformatics team used phred/phrap/consed. On the net, some
people mentioned tracetuner (ex Paracel, now OSS), which also does the job.
Being curious about how differently each program manipulates the trace data, I
made fastq files using all three programs from the same ABI tracefile. In all
3 cases, I used convert_project to convert the exp (pregap4) or
fasta/fasta.qual files (phred and tracetuner) to fastq.
head -n4 pregap/PROJ.fastq
@80301_F_B09
NNNNNNNNNNNTCNNNNNNGGNNANNGANTCCGGCACCCCGGTATTAATGTCGCCGCCGGATAACAACAGGACGCTTCCCCCCTCTTGCGCCACCTCTTTACGGATACTGTCCACCAGCGTTTTTTGCGCTGCCAGACCATATTCGCCATATTCGCTGCGCCAGAAGTGACCGTGGTGATCGTTGGTATGCAGGATAGTAATTTTATAGGTTTTATCTTTTTCGTAAGCCTGTGCAGGCTGAGTCGTCAGCGCGAACGCCGCCAGTAACGCCAGCGCCACACCCCGTTTCAAAAATTTCATCTTTCTCTCCCTGACTCAATATCAACCGCAGAAATTACCTTTCCTTGCAATAATAGACAAATATGTTTTCAGAATTGAGACTTCCTTCAAACACATTTCACAGGTATGTTAGGCAAGTAATAATTACACATCCTACTATCTCCAACATCGCATAAAATTTAAGTGACTTTCTATGGCCATGAGTGAACCAACCCAGCCGTTAGCCGGCGCGCCCGCAGCGGCCGCTAAAGCACGTACTTCGTTTGGTATTTTGGGCGCGATCAGTCTTTCCCATCTGCTGAACGATATGATCCAGTCGCTAATCTTAGCCANNNNNNCCCCTGTNGA
+
%%%%%%%%%%%&(%%%%%%))%%*%%--%/248?ABIHHGIHIKLKKKJJJJLLLLMLLLLKKLLLLLLMMMNNNNOOOOQOOOONNNNNNNNNNNNNNNOOOOONNNNNNNNNNNOOOOOQQQQQQQQQOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOQQQQQQQOOQOQQOOOOONNNNNNNNNNNNNNNNNNNNOOQQQQQQQQQQOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOONNOOOOOOOOOOOONOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOONNNNOOOOOOOOOOQQQQQQQQQQQQQQQQOQOOOOOOONNNNNNNNNNNNNNNNNONOOOOOOOOOOOOOOOOOOOOOOOOOONNNNNNNNNNNNNNNNNMNNNNNNNNNNNNNNOOOOOONNNNNNNNNNNNNMMNNNMMNNMMMMLMLLLLLLLLLLLLLLLKKJJJJJJIJJJJJKLLLLMMMMMMMMMMMMNNNNNNNNNNNNNNMMKKKHGFEEECBCBCBEFFHIJKJJKKKKKKKKKKJJIIJJJJJJIJJJJJJC<72/--%%%%%%*MMMMMM%MM
$ head -n4 traceTuner/PROJ.fastq
@80301_F_B09.ab1 627 8 619
GTCCCAAGTCTCGCATCTGGAGACGGATTCCGGCACCCCGGTATTAATGTCGCCGCCGGATAACAACAGGACGCTTCCCCCCTCTTGCGCCACCTCTTTACGGATACTGTCCACCAGCGTTTTTTGCGCTGCCAGACCATATTCGCCATATTCGCTGCGCCAGAAGTGACCGTGGTGATCGTTGGTATGCAGGATAGTAATTTTATAGGTTTTATCTTTTTCGTAAGCCTGTGCAGGCTGAGTCGTCAGCGCGAACGCCGCCAGTAACGCCAGCGCCACACCCCGTTTCAAAAATTTCATCTTTCTCTCCCTGACTCAATATCAACCGCAGAAATTACCTTTCCTTGCAATAATAGACAAATATGTTTTCAGAATTGAGACTTCCTTCAAACACATTTCACAGGTATGTTAGGCAAGTAATAATTACACATCCTACTATCTCCAACATCGCATAAAATTTAAGTGACTTTCTATGGCCATGAGTGAACCAACCCAGCCGTTAGCCGGCGCGCCCGCAGCGGCCGCTAAAGCACGTACTTCGTTTGGTATTTTGGGCGCGATCAGTCTTTCCCATCTGCTGAACGATATGATCCAGTCGCTAATCTTAGCCATTTTCCCCCCTGTTGA
+
!**2.///6//*339==7A1134-/1217>7DIDDFEEEEE?>=FEDEEEEEEEEEEEEEEHFEEEEEDMMEEEEEEEEEEEEEEEDDEEEEEEEEEEEENDLDEEENDMEEDDEEDJDEEEEEEEEEEEKEEEEEIEEEEEEEEEEEEEEENEEEJEENEENEEEEEIEEEEIEEKEEKEKEEKEEEEEEEDDEEEEEDELHGEIEDCCEEEENEEKKEEEEEEEENEEGDEEEEDDEEEEGDEEEEEEEEEEJEMDEEEEEEEEEEGDNEEEEEIEEEEIEEEGEJEKEEEEEEENEEKEKEEEEEEFGEEEMDEEEKEEKEEEJEHEFEMEEEIGFEEEEDDEEDDDEEEKEEEEEEEEEEEINEEEFDEDEEEEEEDEEELLEEDDEDEEEEEEEEEEEDDEEEEEEEDDEEEEEEEEEEEEDDDDEEDDEFIEEEEEDDEEEEEDDDEEEEEEEEEEEDDEEEEEEEEEGEDDDEDEEDDEEEDDEDDEDEHCDEEEEDDDDDEDEDDCCCDDCCEJHJEEEEEEDDDDDELDEEDDEEEEEEEEEEEEEEEDCCECCDBBDEEEDDDEEEEDDEEIECCIFFDDEEJDGCCEDDEEEEEEEECCCE65**33>??<?EEECF
$ head -n4 phred_files/PROJ.fastq
@80301_F_B09.ab1
AGCCGCAAGGCTCGCATCCTGCGAATCGGATTCCGGCACCCCGGTATTAATGTCGCCGCCGGATAACAACAGGACGCTTCCCCCCTCTTGCGCCACCTCTTTACGGATACTGTCCACCAGCGTTTTTTGCGCTGCCAGACCATATTCGCCATATTCGCTGCGCCAGAAGTGACCGTGGTGATCGTTGGTATGCAGGATAGTAATTTTATAGGTTTTATCTTTTTCGTAAGCCTGTGCAGGCTGAGTCGTCAGCGCGAACGCCGCCAGTAACGCCAGCGCCACACCCCGTTTCAAAAATTTCATCTTTCTCTCCCTGACTCAATATCAACCGCAGAAATTACCTTTCCTTGCAATAATAGACAAATATGTTTTCAGAATTGAGACTTCCTTCAAACACATTTCACAGGTATGTTAGGCAAGTAATAATTACACATCCTACTATCTCCAACATCGCATAAAATTTAAGTGACTTTCTATGGCCATGAGTGAACCAACCCAGCCGTTAGCCGGCGCGCCCGCAGCGGCCGCTAAAGCACGTACTTCGTTTGGTATTTTGGGCGCGATCAGTCTTTCCCATCTGCTGAACGATATGATCCAGTCGCTAATCTTAGCCATTTACCCCCTGTTGAAAN
+
''''((.-0-1,*****5(('''))+24.))*-8A88:FF=JJEEEGPKSSSVZZZZ\ZZLPPPPeeeWSSSSSSeeeeeeeeeeeeeeeeeeeeeeeeeeZZZZZZZeeeeeeeeZZZZZ\\eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee\\ZZZ\\ee\\\eeee_______eeeeeeeeeeeeeeeeeeeee_______eeeeeeeeeeeee________eeeee_ee____eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee__eeeeeeeeee____eeeeeeeeeeeee___eeeeeeeeeeeeeeeeeeeee______eee_____eee___eeeeeeeeeee_______ee_______eeeeeeee________________e____ZZ\\\\\\\eeeeeeeeee\\\eeeeeee\\\\\\\\\\\\\eeeee\\\Z\Z\\\\\\Z\\\\\\\ZZWUZUUU\\\eeee\\e\\\\\\\\\\\eeeeeeeeeeeeee\\\PPLZZLLLP\\\ZZZ\\\\\\Z\\\WWW\\ZZZZZZQ\\\QQ\\\\\\\\QQP8;.0+0*+++44?-)))$!
Who do you trust?
John
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