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Old 08-31-2011, 09:27 PM   #1
dingkai0564
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Default how to use mira to assemble the fastq generated by 454 sequencing

Hi;

I have some questions to use MIRA: I am asking for help about how to use the mira to assemble my fastq file

I had downloaded the fastq file I am interested from NCBI SRA database. But It only provides fastq file. When I read the manual of Mira,

it says another XML file which extracted from the original SFF file to indicate the vector or adaptor information is needed. Since, I only got the fastq file from the internet,can I do the assmble work alone using the fastq file without that XML file.
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Old 09-01-2011, 12:55 AM   #2
nickloman
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You can, but you'd be better off converting the SRA files to SFF using the SRA toolkit and then using them in the suggested way (sff_extract to extract the sequences and clipping information).
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Old 10-26-2011, 03:08 AM   #3
seenstevo
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Hi.
This is the approach I have also been trying to use as I want to use MIRA3 for my assemblies from SRA files. I have used the fastq-dump tool to make fastq files but when i try and use the sff-dump it doesn't work when following the user guide. If you have experience using it I'd really appreciate some help as I may be doing something basic wrong (I am completely new to all things bioinformatics).
Thanks, seenstevo
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Old 10-26-2011, 03:27 AM   #4
sklages
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Quote:
Originally Posted by dingkai0564 View Post
Hi;

I have some questions to use MIRA: I am asking for help about how to use the mira to assemble my fastq file

I had downloaded the fastq file I am interested from NCBI SRA database. But It only provides fastq file. When I read the manual of Mira,

it says another XML file which extracted from the original SFF file to indicate the vector or adaptor information is needed. Since, I only got the fastq file from the internet,can I do the assmble work alone using the fastq file without that XML file.

Usually the 454 created fastq is quality/adaptor clipped.
So why not using them like solexa input data
http://http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_sxa_denovo_solexa_only_assemblies


I don't know what kind of data you have; genomic is straight forward,
cDNA or clone pools (fosmids, BACs) are some different things ...

Last edited by sklages; 10-26-2011 at 03:41 AM. Reason: some of my nonsense removed :-)
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Old 05-25-2013, 04:14 AM   #5
pari_89
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Hi, I am having the same problem. I downloaded a file from SRA and used SRA toolkit to convert it to fastq and sff. But the file can only be converted to fastq. I have only the fastq file which is from ion torrent data and I want to use mira to assemble it? Does anyone know how to do this. I have run mira before with sff file to extract the xml file. I do not know how to do this for fastq file and iontorrent data.

Will be glad if you could help

Thank you.
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Old 05-26-2013, 04:44 AM   #6
GenoMax
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Quote:
Originally Posted by pari_89 View Post
Hi, I am having the same problem. I downloaded a file from SRA and used SRA toolkit to convert it to fastq and sff. But the file can only be converted to fastq.

Thank you.
Do you know if the SFF file is not included in the SRA data or were you not able to extract the SFF file?
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Old 05-26-2013, 01:12 PM   #7
pari_89
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Quote:
Originally Posted by GenoMax View Post
Do you know if the SFF file is not included in the SRA data or were you not able to extract the SFF file?
I have extracted the FastQ file from SRA but there is no SFF available for this file.

Anyway, I have managed to make mira work with fastq file only.

my file was named test_in.iontor.fastq

The commands I used were:

mira --project=test --job=denovo,genome,accurate,iontor --notraceinfo
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