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Old 07-04-2013, 06:37 AM   #1
someperson
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Default Velvet + meta-velvet:which fastq format for paired-end infos?

Hi,
I've been doing some metagenomic assemblies using meta-velvet. I've been using paired-end data for mor reliable assemblies. However, when I wanted to check those assemblies (e.g. using tablet) I could not find the paired end info any-more.
I've recently learned that fastq-formats have changed not only with respect to quality values, but also with respect to paired-end info.

Old format:
@HWUSI-EAS100R:6:73:941:1973#0/1
New Format (that I am using):
@EAS139:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG
(paired-end info bold and underlined)

So Mira for example needs the old format and will just ignore paired-end info it doesn't recognize (without warning!) if you use the new Format.

Does anybody know which Format Velvet and Meta-Velvet use? Are my assemblies now all in reality single-read assemblies?
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Old 07-04-2013, 06:58 AM   #2
mastal
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Default Velvet + meta-velvet:which fastq format for paired-end infos?

I have been using velvet with the new formats of MiSeq and HiSeq PE data, and it works fine.

By the way, in the read that you have used to illustrate the new format, the Y (1:Y:18:ATCACG) indicates a read that has not passed Illumina's QC filter step.

Usually the sequence providers remove those reads.
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Old 07-04-2013, 07:37 AM   #3
muol
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Velvet ignores fastq headers and replaces them with its own (fasta) headers anyway. You just have to make sure that input read pairs are either shuffled in one file, or synced if separate files are used.
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Old 07-04-2013, 08:16 AM   #4
someperson
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@mastal
Thanks, but the example reads I've posted are not mine. they are from the wikipedia page illustrating the differences between the fastq-formats.
@mastal+@muol:
But then how can I check the assemblies with regard to paired-end Infomation? With Mira, for example, I know that you still get assemblies (without error-messages) if you use the wrong format. The assemblies will just in reality be based on single-read assemblies. So how can one really make sure if everything is ok, if the paired-end info is left out from the AMOS-file, the sequence-list and everything? (This just intrigues me. For some contigs i would simply like to check how well supported they are by paired reads. Also a lot of reads are not assembled or dropped from the assembly. I would like to see what has happened to their corresponding partners)

Last edited by someperson; 07-04-2013 at 08:29 AM.
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