[mira_talk] Re: 2 Ways of qualitiy files
- From: Peter <peter@xxxxxxxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sat, 10 Jul 2010 12:58:17 +0100
On Sat, Jul 10, 2010 at 8:40 AM, Philip Stevens <ph.stevens@xxxxxx> wrote:
>
> Hi,
>
> after i got very nice results with my 454 assembly, i got antother set
> of Illumina Reads with *.qual files. My Problem ist that the 454 qual
> files contain such Data:
>
>>F45P5HE01B2554 length=57 xy=0739_0362 region=1 run=R_2009_11_03_09_04_19_
> 37 35 28 28 25 25 25 23 31 32 35 33 32 32 32 33 32 34 34 32 28 18 18 18
> 32 29 29 30 15 16 16 27 24 27 27 23 23 22 21 27 23 23 19 13 13 13 18 16
> 16 25 25 22 17 11 11 11 19
>
>
> i think the standeart 0-40 points scoring for every base.
>
> While i get for my illumina reads a qual scoring looking like this:
>
> @ILLUMINA-52179E_0005:6:36:1047:12976#0/1
> NCCTAGTTGAACTTCTTGATTTTGTATTGATACCAGTTTCACGTGACGGGTGAAGTACAGAGCCAGGATTGGATA
> +ILLUMINA-52179E_0005:6:36:1047:12976#0/1
> BGHIGJOLMM^\^^^[K[P[NLPNJNNNNNVVVVO[WY[[^[`^V]]][]^^]^BBBBBBBBBBBBBBBBBBBBB.
>
> I have information that this is the ASCI2 Score.
What is the ASCI2 score? That looks like the Illumina 1.3+ FASTQ
encoding at first glance, perhaps the older Solexa encoding. See:
http://dx.doi.org/10.1093/nar/gkp1137
> My question: is mira able to use both qualities at a hybrid illumina/454
> assembly? Or have to translate ASCI2 Code into other or way around?
MIRA can cope, and you can tell it the FASTQ offset explicitly if you
don't trust it to work it out automatically.
Peter
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