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Old 11-09-2012, 12:46 PM   #1
Wallysb01
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Default off-line vecscreen for TSA submission

Hi all,

I am in the process of a fairly large submission to TSA at NCBI. I received back a list of sequences to remove due to contamination with non-chordates, mitochondria or vectors. I know I can use the UniVec database to screen vectors locally, but does anyone know of how to reproduce the greater vecscreen that NCBI does after submission. It would be far faster to do this locally, before submitting, then to have to submit, fix it and resubmit.

Thanks
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Old 04-21-2013, 01:53 PM   #2
Wallysb01
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For those who may be wondering:

I never did resolve this. I ended up having to submit all my assemblies through NCBI's TSA submission process and clean them after I got them back. It was a real pain. I don't understand why NCBI doesn't just trim for you if they go through all the trouble to screen it.
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Old 01-20-2014, 02:11 PM   #3
elli
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Dear all, I have a question concerning VecScreen outputs. I was using blastn to determine Vector contamination on my Illumina data set. Luckily I got it to work. But now I face the interpretation of the output files....

- I used output format: -outfmt 6 and I got this:
HWI-ST827:98:C0C3WACXX:8:1101:2315:2020 gnl|uv|M13163.1:477-1287 100.00 1624 611 626 352 32.2
HWI-ST827:98:C0C3WACXX:8:1101:2731:2019 gnl|uv|U09128.1:1-1663 100.00 16 0 19 34 685 700 352 32.2
HWI-ST827:98:C0C3WACXX:8:1101:2920:2121 gnl|uv|U67875.1:18-1316 100.00 16 0 41 56 384 399 352 32.2
HWI-ST827:98:C0C3WACXX:8:1101:2816:2171 gnl|uv|L05081.1:2594-3343 100.00 1615 30 572 557 352 32.2

I really would appreciate any help to name the columns.
Thank you so much.
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Old 01-20-2014, 03:23 PM   #4
GenoMax
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That looks similar to the output from the blast outfmt 6: http://drive5.com/usearch/manual/blast6out.html Logically seems to be correct but can't find a definitive source on vecscreen site.
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