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Old 11-07-2009, 09:11 AM   #1
cliff
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Location: USA

Join Date: Oct 2009
Posts: 41
Default Maq reads split problem

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:

s_1_1_sequence@1.bfq
s_1_1_sequence@1000001.bfq
s_1_1_sequence@2000001.bfq
s_1_1_sequence@3000001.bfq
s_1_1_sequence@4000001.bfq

I understand these four files:

s_1_1_sequence@1000001.bfq
s_1_1_sequence@2000001.bfq
s_1_1_sequence@3000001.bfq
s_1_1_sequence@4000001.bfq

are the output split files. But I don't know what "s_1_1_sequence@1.bfq" is.
I tried this command on read 2 from the same land and got the same problem. It output "s_1_2_sequence@1.bfq". 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
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