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Old 05-27-2010, 02:11 AM   #1
mmanrique
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Default Error in contigs length in 454AllContigs.fna 454 Output file

Hi there,

Checking out the 454 output file 454AllContigs.fna I've found out some errors in contig length. There are some cases where the contig length written in the fasta header is clearly different from the actual contig length, sometimes bigger, sometimes smaller. An example

>contig04402 length=72 numreads=580 gene=isogroup00010 status=isotig
ttgtattgaatgcactgaTCTGGGGTgAGAAATCTTCTGGTGCTgtACCTTTTGGGACTA
TGTTTGCTTtGGTcTTTTTGtGGTTtGGAATTTCCGTGCccTtGGTTTTTATTGGCAGct
ACTTTGGCTACAAGAAACCTGCAATTGAagATCCAGTGAAAACAAACAAAATTCCCAGGC
AAATT



Does anyone know what could be happening?

Thanks

Marina
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Old 05-27-2010, 01:54 PM   #2
pr0t3us
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I have the same problem using newbler with cdna option.
I have already write to penzberg and they answer me that this is probably a bug
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Old 05-28-2010, 01:52 AM   #3
mmanrique
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Hi pr0t3us,

thanks very much for your reply. It's good to know it's a bug

Marina
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Old 07-15-2010, 12:39 AM   #4
neolith
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The length is not of contigs, bua of isotigs.
lenght=72 mean that in the contig04402, only 72bp used in isotigs.
anywhere... that is just a bug.
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Old 07-21-2010, 05:51 AM   #5
robertorun
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i also find the bug, but i email to 454 Roche company and don't get the answer.

Through comparision, the lenght=72 maybe the length longer than another contig from the same isotig. For example, the following is part of Newbler result,contig00919's length is 491, that is right. But, the length of contig02971 is 216, it's error, the actual length of contig02971 is 707, just 491+216=707. The blast result also show the former 491 bp are the same bettween two contig.



>contig00919 length=491 numreads=9 gene=isogroup00335 status=isotig
TtGgAGGAGCCAaGGgCATCTCTCTCATACACACAaGCACTATATTATaTGTATATGATT
GAGCTAAGGCAGTTGCAGGAATTATCTGTGTATaTATTATtATGTACATTATGTTCaTaC
AaTTAAGTTTAAAAGATGCAACACCTCACCaCTAAACCCTTTTgATCAATCCtCGCCTCA
TCATTGCCTTCaGGAGGCTGAGTAAGCTTCCGgTTTTgTGGAGACATCATTTCTTTCTtC
AGCTGAGTCAATATATCCTCCATTGTATaCTCCCTTCGCCAATTAGCAAGCATGGGGAAA
AGGCTTGGTTCAACCACTTTGGTTTCGGgATTGACACAGGTCATATTTATCCGGGTTTGA
AACCTCACGCTCGGTGGGTTATCGGgATAATCCATGCCACAGAACAATTTCAACTGGTAG
ATGCGTCCTtCATGAaCAGTATTAGGgGGgCCgaTAATAGTGCcAGTCCACGATTGCATG
TATACTtCATC
>contig02971 length=216 numreads=21 gene=isogroup00335 status=isotig
TtGgAGGAGCCAaGGgCATCTCTCTCATACACACAaGCACTATATTATaTGTATATGATT
GAGCTAAGGCAGTTGCAGGAATTATCTGTGTATaTATTATtATGTACATTATGTTCaTaC
AaTTAAGTTTAAAAGATGCAACACCTCACCaCTAAACCCTTTTgATCAATCCtCGCCTCA
TCATTGCCTTCaGGAGGCTGAGTAAGCTTCCGgTTTTgTGGAGACATCATTTCTTTCTtC
AGCTGAGTCAATATATCCTCCATTGTATaCTCCCTTCGCCAATTAGCAAGCATGGGGAAA
AGGCTTGGTTCAACCACTTTGGTTTCGGgATTGACACAGGTCATATTTATCCGGGTTTGA
AACCTCACGCTCGGTGGGTTATCGGgATAATCCATGCCACAGAACAATTTCAACTGGTAG
ATGCGTCCTtCATGAaCAGTATTAGGgGGgCCgaTAATAGTGCcAGTCCACGATTGCATG
TATACTtCATCAGCATCATCCATTCCATAGCTAACAGTTCCATCCCCAATtCcTTTTtCA
CCTCTCtCgaGTtCTTCtaGCAATCTGAAATTCCtaGGCACAaCAACactcGATCCTTCA
GAACCCATTCCTTCTcttGATCGTTCAAAAcAAAGAGATtAaGAATtAGGgTTTTTTttC
TCTGATTTCAAAAGCGAAAgCCCAaAAATAGtaGAGAGGAAAaTCAA
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