Hello everyone,
I notice there has been the odd post about this general topic before but I am still confused!
I have SOLiD single and paired end data which I would like to take through the following steps:
1) Quality assessment - Fastqc
2) Data cleaning - Quality trimming/removing adapters if necessary
3) Mapping using BWA
At the moment I am converting the csfasta and qual files in to double-encoded (fakespace) fastq files for BWA. I reverse the F5 reads so BWA treats them correctly. However, can the same fastq files be used with Fastqc? Also, can CutAdapt and fastq_quality_trimmer handle this format? If anyone else out there still uses SOLiD data and can give me some details of their workflows I would be very grateful.
Best wishes,
Kath
I notice there has been the odd post about this general topic before but I am still confused!
I have SOLiD single and paired end data which I would like to take through the following steps:
1) Quality assessment - Fastqc
2) Data cleaning - Quality trimming/removing adapters if necessary
3) Mapping using BWA
At the moment I am converting the csfasta and qual files in to double-encoded (fakespace) fastq files for BWA. I reverse the F5 reads so BWA treats them correctly. However, can the same fastq files be used with Fastqc? Also, can CutAdapt and fastq_quality_trimmer handle this format? If anyone else out there still uses SOLiD data and can give me some details of their workflows I would be very grateful.
Best wishes,
Kath
Comment