Hello
I just got a question. I wanna align SOLID data with BWA and therefore transformed it in FASTQ files with the solid2fastaq.pl script. But the script does not take the whole sequence of the csfasta but excludes the first two bp. In my opinion it would make sense to exclude the first base, as it is not in color space but not two.
Here an example:
an entry of my csfasta files has following sequence
>1_3_123
T000111222333
and the output in the FASTQ file is a sequence with:
AACCCGGGTTT
By comparing the sequences it can be seen that two bp are missing:
T000111222333
AACCCGGGTTT
this is because of line 100 in the script delivered by BWA 0.5.7 in the method read1:
$_ = substr(<$fhs>, 2);
This funktions takes the sequence beginning from the 3rd position.
Is there any reason for this or is this an error ?
Thanks for answering
martin
I just got a question. I wanna align SOLID data with BWA and therefore transformed it in FASTQ files with the solid2fastaq.pl script. But the script does not take the whole sequence of the csfasta but excludes the first two bp. In my opinion it would make sense to exclude the first base, as it is not in color space but not two.
Here an example:
an entry of my csfasta files has following sequence
>1_3_123
T000111222333
and the output in the FASTQ file is a sequence with:
AACCCGGGTTT
By comparing the sequences it can be seen that two bp are missing:
T000111222333
AACCCGGGTTT
this is because of line 100 in the script delivered by BWA 0.5.7 in the method read1:
$_ = substr(<$fhs>, 2);
This funktions takes the sequence beginning from the 3rd position.
Is there any reason for this or is this an error ?
Thanks for answering
martin
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