[mira_talk] Re: Vector trimming
- From: Jeremiah Davie <jdavie@xxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 15 Jul 2010 15:47:03 -0400
Hi Praveen,
I can't speak to #1, although I do believe that topic is covered
very well in the new docs. As for #2, I believe MIRA accepts the fastq
format for 454 data, so I don't think you need to go to that much
trouble - Jeremiah
On Jul 15, 2010, at 3:36 PM, Raj Kumar, Praveen Kumar Mr. wrote:
Hi,
I have two questions here. First of all, I am trying to assemble
the 454 ESTs.
[1] I like to use the contaminant trimming option for my 454
sequences. My question is will mira accept txt file (contain adapter
sequences in fasta format) as adapter database?. My next question is,
[2] The quality file I have is of the format below
SRR057469.1 F3GWPE201DS5Z5 length=40
FFFFFFFFFFFDDA:::::DDDBBBAAEFFDAA>A???80
SRR057469.2 F3GWPE201BYIZ0 length=55
FFFFFFFFFFFHHFHFFCCEFFFFECCFFGFFFFFFFE@??BBAA=;<;1412--
That is quality values are as such present in Fastq file. I used AWK
+SED scripts to generate quality file from FASTQ like this,
$ awk '(NR%4==1) || (NR%4==0)' INPUT.FQ | sed 's/^@/>/' >
qualities.txt
Here my question is, is this acceptable for mira?
regards,
Praveen
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