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Old 06-01-2010, 01:00 PM   #1
jjw14
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Location: Missouri

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Question Reduce file size after Illumina FASTQ to Sanger FASTQ conversion?

Hi,

Great forum! My first post:

I have Illumina 1.3+ FASTQ files that I am converting to Sanger FASTQ using maq as follows:

maq sol2sanger s_1_sequence.txt s_1_sequence.fastq

It runs fine, but after the conversion is done, the file size has been reduced from 4.6 GB (4615468 bytes) to 3.5 GB (3556236 bytes). Is this simply due to the change in the Phred quality score ASCII character length for each read in the file?

I just wanted to make sure I wasn't losing actual sequence data.

Thanks very much in advance,
jjw
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Old 06-01-2010, 02:43 PM   #2
Jon_Keats
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Default

The read ID information is no longer duplicated for both the read and quality information such as

My Read1
AGTC
My Read1
#$%@^

Becomes

My Read1
AGTC
#$%@^
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Old 06-01-2010, 04:35 PM   #3
jjw14
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Thumbs up

Thanks very much.
jjw
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