Maq reads split problem

[cliff]

Hi, All

I just got a problem when splitting 4M reads from read1 in one lane (Illumina GA) into 1-million chunk. I tried:

maq fastq2bfq -n 1000000 s_1_1_sequence.fastq s_1_1_sequence

and I got 5 output files:

[email protected]
[email protected]
[email protected]
[email protected]
[email protected]

I understand these four files:

[email protected]
[email protected]
[email protected]
[email protected]

are the output split files. But I don't know what "[email protected]" is.
I tried this command on read 2 from the same land and got the same problem. It output "[email protected]". It also happens to all the other flow cells.

Also, when I changed it to 2-million chunk, I still got this @1.bfq file.

I checked the size of this @1.bfq file and it is similar to the other @1000001. bfq or other .bfq output files.

Can anybody tell me what this @1.bfq file is? Should I remove it for further mapping?

Thanks in advance

-Cliff

[ECO]

@1... is just the first batch of split reads. (Which is why it's the same size as all the rest, save for the last one, which is variable in size depending on how many reads you have left over in relation to the (#reads)/(split size).

So, you want all 5 files.