[wgs-assembler-users] Converting IIDs to Read Names from FASTQ files

[Arjun P. <ap...@ma...>]

Hi,

I need to get a read-mapping with the actual read-names for an assembly 
that was created based on FASTQ input sequences. I noticed the iidtouid 
file in the 9-terminator directory, but it has numbers for fragments 
rather than read names.

Looking at the reads from the 9-terminator/.frg file I matched up some by 
sequence, and it looks like the FRG numbers are alternating reads from 
each of the paired ends.

e.g.,

     FRG 1   110000000001 - first entry from read 1
     No FRG 2
     FRG 3   110000000003 - 2nd entry from read 1
     FRG 4   120000000003 - 2nd entry from read 2
     FRG 5   110000000005 - 3rd entry from read 1
     FRG 6   120000000005 - 3rd entry from read 2
     FRG 100000 120000099999 - Entry 50,000 from read 2

I'm guessing that I can figure out the read name to iid translation by 
counting into the fastq files by FRG # / 2

Has anyone else done this? Did I correctly interpret what the FRG numbers 
mean? Are there any gotchas at input file boundaries?

Thanks,
Arjun

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