Reduce file size after Illumina FASTQ to Sanger FASTQ conversion?

jjw14 · 06-01-2010, 02:00 PM

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

Jon_Keats · 06-01-2010, 03:43 PM

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
#$%@^

jjw14 · 06-01-2010, 05:35 PM

Thanks very much.
jjw

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06-01-2010, 02:00 PM	#1
jjw14 Member Location: Missouri Join Date: Apr 2010 Posts: 39	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

06-01-2010, 03:43 PM	#2
Jon_Keats Senior Member Location: Phoenix, AZ Join Date: Mar 2010 Posts: 279	The read ID information is no longer duplicated for both the read and quality information such as My Read1 AGTC My Read1 #$%@^ Becomes My Read1 AGTC #$%@^

06-01-2010, 05:35 PM	#3
jjw14 Member Location: Missouri Join Date: Apr 2010 Posts: 39	Thanks very much. jjw