Dear users,
I have PE reads from SOLiD to align to human genome.
I have these files:
- solid_data_F3.csfasta
- solid_data_F3_QV.qual
- solid_data_F5-P2.csfasta
- solid_data_F5-P2_QV.qual
I want to convert in fastq these files by using bwa0.5.7/solid2fastq.pl
This script runs only for F3 but with F5-P2 the program doesn't run. (it says Fail to open solid_data_F5-P2_F3.csfasta)
So, if I use:
> solid2fastq.pl solid_data_ solid_data_total
I generate only one file fastq for F3 and F5-P2. It includes all the paired-end?
This fastq is in colorspace but the colors are represented as ACTG.
So to index the genome and to perform bwa alignment, have I to use -c option?
Thanks a lot,
ME
I have PE reads from SOLiD to align to human genome.
I have these files:
- solid_data_F3.csfasta
- solid_data_F3_QV.qual
- solid_data_F5-P2.csfasta
- solid_data_F5-P2_QV.qual
I want to convert in fastq these files by using bwa0.5.7/solid2fastq.pl
This script runs only for F3 but with F5-P2 the program doesn't run. (it says Fail to open solid_data_F5-P2_F3.csfasta)
So, if I use:
> solid2fastq.pl solid_data_ solid_data_total
I generate only one file fastq for F3 and F5-P2. It includes all the paired-end?
This fastq is in colorspace but the colors are represented as ACTG.
So to index the genome and to perform bwa alignment, have I to use -c option?
Thanks a lot,
ME
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