[mira_talk] 454 cleaning
- From: Robin Kramer <kodream@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 11 Nov 2010 10:43:55 -0700
Hi,
I am doing an assembly from data publicly available at NCBI.
The data are available here:
http://www.ncbi.nlm.nih.gov/sra/SRX021565?report=full
It is 454 data, but unfortunately neither the sff or xml files are available.
I assembled the data with Mira, using the no xml flags.
Which appeared to give a nice assembly.
However when I BLASTN and BLASTX the first and forth contig their
appear to be problems with the data.
With the first contig, when I blastx it, it gives strong hits to two
different genes on different ends, as if it were a chimera. When I
blastn the sequence I get a strong hit on one side, then in the middle
I get section with multiple hits to different species in the TSA.
When I look at the pileup, there is a thin place in the gene an a huge
drop off in coverage from one side.
I think this appears to be due to a adapter trimming problem with the 454 data.
The fourth contig when blastN has a very strong gene hit from a
closely related species, but at the end has another small stretch that
matches many other sequences in TSA that are distantly related. The
adapter looking portion has small coverage with a giant change in
coverage in the strong region.
To me it appears as if some of the adapters are consistently not
getting trimmed(in this set and in TSA).
Here is a relevant thread in seqanswers.
http://seqanswers.com/forums/showthread.php?t=3462
As well as a link out to previous discussions in this list.
//www.freelists.org/post/mira_talk/454-adaptor-clipping
Is there any consensus on recleaning the 454 adapters? I don't even
know what the sequences would be to expect.
The assemblies of the two contigs are pasted after this message.
Sincerely yours,
Robin
>SRR054580_Asha_rep_c1
AGTTTCTTAACACTTGGACCAATATATTATTTTCCTTTGTTTTGCAAGAAGGATAAAAGA
AAGAAACAAASGWMDAAAAGAGTTTACTAGAAAACTCATCGAGCTAGTTTCTCCACTTAT
TTATTTTATGCTTTTCCCGCAAAAGTTTGGTGACTCATACATGAGGATAGATACACATAG
ACTCACGTTATTTTACACACGTATATATATAAGGAAAGGCAGGCTAAGCCTTTGATTTAT
TTGATTATTGATCCGCGCACTATTGGCAAAAAGACAGTAGTGGGGTAGCACAGCAGATGC
AAAAAGATGAAGCATAGCTCTAAGCCACATATCTCATTTGAGAGTGACGAGGAGGTGGAA
CGAGAAAGTTGAAAGGGTTGTTGTTCTTGATCTGCCTGGCCTGTTCGCTATGGAGGTTGA
AAGTGTGTTGAATGACTTCCTCAGGCAATGCGTTTAACAAAGAGTTTCTACCTGCAAGTG
TGCCAGTCACAGGTATATCATGGGTCTTGAATGCCACGTACTTGAAGTTGTTGCTCTGCG
ATTTTGCAGCCACCGCAAAGTTTTGTGGCACGATCAGCACTTGTCCCTCTTGCAGCTCCC
CATCAAACACTCTATCACCAGTGCAATTCACCACTTGCATCATCGCCCTCCCTTCCAATG
CGTATACTATGCTGTTTGCGTTCAGGTTGTAGTGAGGCACGAACATGGCATTCTTGCGGA
GAGATCCGAACTGAGCACTGAGTTTGAGGAGCAAGAGGGCTGGGAAGTCAAGGCCGGTGG
CGGTTGTAATGCTACCAGCTTGAGGGTTGAAGAAGTCAGGCGATGAAGTTTGACCAATGT
TGTGGCGAAGTCTCATTGTGCAAATGGTTTCATCAATGCCATTTCTGCTCTTGCTTTTGC
TCTTCTGTGGCTTCTCTTCCTCTTCATCGTCGTCATCTTCTTCCTCTTCCTCTGCTCTCT
GTTGCTGCTTTCTCGTTGGTGGAGCTGTCACGCTCAGACCTCCCTCCACTTTCACAATGG
CTCCTTTCTCTTCGTCCTCGTTCACACCTTGGAGGTTTTTCACTATCTTCCTGTCCACGT
TCAACGCTTGTTCCAAGAATTCTGGGGTGAAGCCACTGAATATGTTGCCGCCTTCATTAT
CTTCTTCTTGTTCTTGATGTTGTTTTCCCTTCTGGCTTTGGCTTTGCTGATATTGTACGA
ACTCTTGCTCTTGGTTCCCAGCAAGATAGAATCTCCTAGGCATCTGATCGAGCTGGTTCT
GTAAGCTGTTGGTGTGAATAAGAGAAACTGCAACAACGGGAGTGTCTTGATTGTTGAACA
TCCAGAAAGCAGCACCGGTAGGCACTGCGATCAAATCACCCTCTCTAAAGTGATACACCT
TTTGGTGACGGTCTTGAGGCTTCTGGCTTTGTCCTCTTTGAGTTGGCTCTTCAAAAGTCT
GAGGACAACCGGAGAAAATGATGCCAAAAATACCACTACCTTGTTGAATGAAGATTTGCT
GGGGAGCGTTGGTGAAGAATGGTCTGCGGAGGCCATTGCGTTGGAGGGTGCAGCGAGAGA
GGGCAACACCGGCACACTGGAAAGGCTTGCTGTTAGGGTTCCATGTCTCTATGAACCCAC
CTTCCGACTCTATACGGTTATCGGGTTTGAGGGCATTCATGCGTTGGAGTTGGCACTCAT
ATTCATTTTGCTGTGGCTGCTGTGTCTTATCTTTGCTAGCGAAGCACCCACTCAAAAGCA
CAAGACAAAGGGAAAGAGATAGCGCAAGAAGCTTAGCCATGGATATGAATATGATTGATT
TGTTTGTGGTGTCCCCCGTACTCTGCGTTGATACCACTGCTTAAGCAGTGGTATCAACGC
AGAGTACGGGGGTGGACCCAATGACACCATTTTCATTTATTATTCGGATCATGGTGCTCC
TGGTCTTGTCACCATGCCAGTAGGGGGAATATGTCATGGCCAACGATTTTGTGAATGTCT
TGAAGAAGAAACATGATGCTAAATCCTACAAAAAGATGGTGATATACTTGGAAGCATGTG
AATCTGGGAGCATGTTTGAAGGGATACTACCTAATAACATAAGCATATATGCGACCACAG
CTTCCAACGCAGATGAGGATAGTTTTGCATATTATTGTCCTCATTCCTACCCTTCTCCTC
CAACTGAGTACACCACTTGTTTGGGAGATGTGTACAGCATTTCGTGGTTAGAAGATAGTG
ACAAAAATGACATGACAATAGAAACGCTGCAGCAACAATATGAAACCGTTCGCCGAAGAA
CGTTAATTGGTAATGTCGACACCTCTTCTCATGTGAAACAATACGGAGATAGAAAATTCG
AGAACGATACTCTTGCTACCTACATTGGTGCACCTGTTAAAACCAACCCCACCAACTCTG
CAAATGCATATTCCTTTGAACCATATAGTCCTCAAACTAGACATGTTAGCCAACGAGATG
CTCATTTACTCTACCTTAAGCTAGAGTTGCAAAAAGCCCCGGATGGTTCTATGGAAAAGT
TGAAAGCTCAAATAGAGTTGGATGATGAAATTGCACATAGGAAGCATTTAGATAGTGTTT
TCCATCTCATAGGGGATCTCTTGTTTGGAGAAGAGAATAATATCTCTACCATGTTGCTCC
ATGTTCGTCCACCAGGCCAGCCTCTTGTCGATGATTGGGATTGTTTCAAGACCCTTATAA
AAACTTACGAGAGCAATTGCGGTAAATTGTCAATCTATGGAAGGAAATACACAAGAGCCT
TTGCTAACATGTGCAATGCTGGCATTTCTGAGGAGCAAATGGTAGTAGCCTCTTCACAAG
CTTGTCCCAAGGAAAATCCTTCTTAAATTAATTCGTTAAGTTGATAATGTAATAACCAAT
ATATATCATGAAAGATTAAAAATTGTGCTTTCATTCTACAAAATGGATTATAATCCTTTG
>SRR054580_Asha_rep_c4
TCTCCGACTCAGAAGCAGTGGTATCAACGCAGAGTCTTGGGGAACTGGAATTGACGATCA
AGTTGGTCACACCTGTTGCTCCAGCAACATAGTGCAGAAATTGCATGTGTCCAATGTGTA
GATCTCTAACAAGATCATAATTATAACATTCTATGTGTAGTTGACTCTTGCTTTTGATTA
ACTCCTGCATAGATGTTTCTACCAAAAATGAAAAAAAAAATCATTAATAGATGCATATTG
CAGCTAAATTTAGCAGTGAGTTGGTGATACCTCATCCCCCAGTTAGATAAAAGCCACTAG
AAGCTGCATTTTCAAATCAACAAGTAGTGATTTATGGCTTCTTTGGGTTTTATGGTGTGT
TTTGTAGAAAATTTGTCCTTCATTTTAGCTATGAGCATTCATTGGGTATTGCATAAGTTT
TGATGCTATTGTATTGATTTTGATATAAGAAAAGAAAAGTTGTAATGCGTTTGTTTCAAT
TATTTTTTTTTAAAGAAATGATATTTTTAACTTGTGGAGAGTTTTAAGAGATTTAGATAA
CTTGTAAGGTAACAGATTGTAGAAGTATAAATTACTCTGCCATAAATGAAGCTTTAAGTG
CACTACAAGTAAACAACT
--
You have received this mail because you are subscribed to the mira_talk mailing
list. For information on how to subscribe or unsubscribe, please visit
http://www.chevreux.org/mira_mailinglists.html
Other related posts:
