I am currently working with SOLiD RNA-seq NGS data from 2013. I was provided 48 .csfasta and .qual files from my PI (24 F3 files and 24 F5 files)- I used galaxy's solid2fastq tool (called Convert SOLiD output to fastq: https://usegalaxy.org/?tool_id=solid2fastq&version=1.0.0&__identifer=3y01dzhi3ya) to create 24 .fastqcssanger files (12 F3 and 12 F5). I ran a FastQC on these files and almost all of them had traces of ABI Solid3 Adapter B in them in the overepresented sequences. I want to remove these adapters, naturally, before moving on to alignment.
I was able to find the sequence of this adapter on https://github.com/csf-ngs/fastqc/blob/master/Contaminants/contaminant_list.txt but I also was given a sequence for it on galaxy through FastQC: which sequence should I use in an adapter removal program?
My next question was which tool should I use to trim this SOLiD adapter? I have been trying cutadapt for quite a while now and I keep getting an invalid syntax error over and over (SyntaxError: invalid syntax). I have been trying the following code and I have been unable to get any success:
1) "/usr/bin/python" to initialize our Python (the system properly loads Python)
And then one of the following (note below that the adapter sequence I have been entering has been from the fastqc website, not the one from the FastQC overrepresented sequence- hence the above question) :
2a) "cutadapt -c -a CCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGAT '/home/WMurphy/Documents/Chondrocyte NGS/I3_2013_02_01_F5-RNA.csfasta' '/home/WMurphy/Documents/Chondrocyte NGS/I3_2013_02_01_F5-RNA.QV.qual' > output.fastq"
- 2b) "cutadapt -c -a CCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGAT '/home/WMurphy/Documents/Chondrocyte NGS/I3_2013_02_01_F5-RNA.csfasta' '/home/WMurphy/Documents/Chondrocyte NGS/I3_2013_02_01_F5-RNA.QV.qual'"
- 2c) "cutadapt -c -a CCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGAT '/home/WMurphy/Desktop/I3_F5.fastqcssanger'"
- 2d) "cutadapt -c -a CCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGAT '/home/WMurphy/Desktop/I3_F5.fastqcssanger' > output.fastq".
Nothing has worked. I have been rereading http://cutadapt.readthedocs.io/en/stable/colorspace.html over and over, and I still don't know what I am doing wrong. Any and all help would be immensely appreciated!
Have a great day!