Hi,
I'm trying to convert my SOLiD reads to FASTQ using BFAST+BWA's solid2fastq.pl utility. I have two sets of paired-end files
However, the solid2fastq.pl utility only allows files labeled F3 and R3
The SOLiD documentation (see here), however, says that F5 is for paired end and R3 is for mate-pair. My reads are paired end and so they are labeled F5.
My question is how do you go about merging these two files? Is it as simple as renaming the F5-DNA files as R3? I also notice in the documentation that F5 and R3 are in opposite orientation. Is it then required to reverse-complement the F5 reads to make them R3? How is that done? Am I missing something?
If solid2fastq cannot accomplish this task, do you know of any other programs which could do this? Finally, I want to:
1) Trim adapters from each paired-end file individually using cutadapt (which takes a FASTQ file)
2) Map the filtered reads using BFAST (which also takes a FASTQ file)
Thanks
I'm trying to convert my SOLiD reads to FASTQ using BFAST+BWA's solid2fastq.pl utility. I have two sets of paired-end files
*_F3.csfasta
*_F3_QV.qual
*_F5-DNA.csfasta
*_F5-DNA.QV.qual
*_F3_QV.qual
*_F5-DNA.csfasta
*_F5-DNA.QV.qual
Note: <in.title> is the string showed in the `# Title:' line of a
".csfasta" read file. Then <in.title>F3.csfasta is read sequence
file and <in.title>F3_QV.qual is the quality file. If
<in.title>R3.csfasta is present, this script assumes reads are
paired; otherwise reads will be regarded as single-end.
The read name will be <out.prefix>: panel_x_y/[12] with `1' for R3
tag and `2' for F3. Usually you may want to use short <out.prefix>
to save diskspace. Long <out.prefix> also causes troubles to maq.
".csfasta" read file. Then <in.title>F3.csfasta is read sequence
file and <in.title>F3_QV.qual is the quality file. If
<in.title>R3.csfasta is present, this script assumes reads are
paired; otherwise reads will be regarded as single-end.
The read name will be <out.prefix>: panel_x_y/[12] with `1' for R3
tag and `2' for F3. Usually you may want to use short <out.prefix>
to save diskspace. Long <out.prefix> also causes troubles to maq.
My question is how do you go about merging these two files? Is it as simple as renaming the F5-DNA files as R3? I also notice in the documentation that F5 and R3 are in opposite orientation. Is it then required to reverse-complement the F5 reads to make them R3? How is that done? Am I missing something?
If solid2fastq cannot accomplish this task, do you know of any other programs which could do this? Finally, I want to:
1) Trim adapters from each paired-end file individually using cutadapt (which takes a FASTQ file)
2) Map the filtered reads using BFAST (which also takes a FASTQ file)
Thanks
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