MG-RAST - header format problem?

[mstagliamonte]

Hi everyone,

after successfully using MG-RAST with assembled data, I am trying to use it with raw fastq illumina sequences. I originally had two fastq files (forward and reverse paired ends); I merged them and uploaded the file.

I now receive an error message:
Warning: The unique id count does not match the sequence count. You will not be able to use this file for submission.

Basically the unique id count is half the number of sequences.
My reads are ordered as forward and reverse with the following format:

@HWUSI-EAS1700R:25:FC:6:1:12466:1106 1:Y:0:TTAGGC

and

@HWUSI-EAS1700R:25:FC:6:1:12466:1106 2:Y:0:TTAGGC

My guess is that I may need to modify the header. Any suggestion?

Thanks
Max

- Edit: I should be able to modify the header by myself (I know a little bit of Python), but I am not sure if that is the problem and what my header should be.
Thanks again
Max

[Ciaran]

Only the first part of the header is being used to identify the read,
Just replace the space with a "_" or other character.


instead of;
@HWUSI-EAS1700R:25:FC:6:1:12466:1106 1:Y:0:TTAGGC

have

@HWUSI-EAS1700R:25:FC:6:1:12466:1106_1:Y:0:TTAGGC

Something like

sed 'e/\ /\_/g' seqfile > seqfile_ed

[mstagliamonte]

Thanks,

I'll try immediately and let you know.

Regards,
Max

[Ciaran]

sorry,

sed 's/\ /\_/'

[mstagliamonte]

Hahaha,

I noticed

I was not able to fix it, so I've just started running my python script.

Let's see how it goes

[mstagliamonte]

Hi, Ciaran,

many thanks for your advice, it worked.

Have a nice day
Max