Hello, does any one know what is the difference between these two maq scripts (both available in the latest maq version 0.7.1):
sol2sanger
sol2sanger convert Solexa FASTQ to standard/Sanger FASTQ
Usage: maq sol2sanger in.fastq out.fastq
sol2std
sol2std Convert Solexa/Illumina FastQ to the standard/Sanger FASTQ
Usage: pearl fq_all2std.pl sol2std in.txt > out.fastq
I tried both scripts with the file "_sequence.txt" that I got from the Illumina. Here are the results for the first sequence:
s_sequence.txt
@GAII01_3:8:1:136:1560
GAGTTCAATTTTGTTAATTCCTTTCTGAAAATAGAT
+GAII01_3:8:1:136:1560
WWWWWWWWWWWWWWWWWWWWWWWWWWLWWWRRRIRO
sol2sanger_s_sequence.fastq
@GAII01_3:8:1:136:1560
GAGTTCAATTTTGTTAATTCCTTTCTGAAAATAGAT
+
88888888888888888888888888-888333+30
sol2std_s_sequence.fastq
@GAII01_3:8:1:136:1560
GAGTTCAATTTTGTTAATTCCTTTCTGAAAATAGAT
+
88888888888888888888888888-888333+30!
The only difference between the fastq file generated by sol2sanger and sol2std scripts is that the sol2std writes a "!" in the end of the 4th line..
I checked, it does this in every 4th line of the file..
What does this means?
What script is the best?
Thanks!
Ines de Santiago
sol2sanger
sol2sanger convert Solexa FASTQ to standard/Sanger FASTQ
Usage: maq sol2sanger in.fastq out.fastq
sol2std
sol2std Convert Solexa/Illumina FastQ to the standard/Sanger FASTQ
Usage: pearl fq_all2std.pl sol2std in.txt > out.fastq
I tried both scripts with the file "_sequence.txt" that I got from the Illumina. Here are the results for the first sequence:
s_sequence.txt
@GAII01_3:8:1:136:1560
GAGTTCAATTTTGTTAATTCCTTTCTGAAAATAGAT
+GAII01_3:8:1:136:1560
WWWWWWWWWWWWWWWWWWWWWWWWWWLWWWRRRIRO
sol2sanger_s_sequence.fastq
@GAII01_3:8:1:136:1560
GAGTTCAATTTTGTTAATTCCTTTCTGAAAATAGAT
+
88888888888888888888888888-888333+30
sol2std_s_sequence.fastq
@GAII01_3:8:1:136:1560
GAGTTCAATTTTGTTAATTCCTTTCTGAAAATAGAT
+
88888888888888888888888888-888333+30!
The only difference between the fastq file generated by sol2sanger and sol2std scripts is that the sol2std writes a "!" in the end of the 4th line..
I checked, it does this in every 4th line of the file..
What does this means?
What script is the best?
Thanks!
Ines de Santiago
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