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Old 08-24-2012, 12:16 PM   #1
mirex
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Location: sao paulo

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Default extend sequence

Hello,
I have paired end reads Illumina and I need to complete a sequence of bacteria, i have only 4kbp, I would complete the ends of a bacterial sequence, I have only 4kbp, for that I'm using Novoalign trying to lengthen the ends doing a loop with the previous results, anybody can give me better ideas?
I would also like to know what you mean trim consensus sequences to 4x coverage from pileup file. Sorry, I'm new in this work, how I do this?, delete lines that have a greater coverage to 4?, is there a program for this?
Thanks,
Mirex
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Old 08-25-2012, 09:04 PM   #2
krobison
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Could you explain in more detail what you do have? Shotgun Illumina data for your entire organism? How was the library prepared? Do you have an estimate of the genome size & what coverage you have.

What is the 4Kbp -- a gene of interest?
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Old 08-28-2012, 10:59 AM   #3
mirex
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Hi, thanks a lot for the reply!. The data is FASTQ Illumina 1.3+ paired-end, about entire plant, but 7kbp is an estimated of gene of interest and for now i have only 4kbp.
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