Hello,
I would like to generate a fasta file containing unique reads and count of each read occurrence, from two Illumina fastq files (forward and reverse). The next step is to blast the unique reads and group them together based on the results of the blast search. Could someone please suggest a tool that could accomplish this?
Thanks
2 answers
You need clumpify.sh from BBMap suite to remove/count duplicate reads. See this: A: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files
Once you have your set of unique fastq reads they can be easily converted to fasta format by using reformat.sh from BBMap suite. I am reasonably certain that the read header containing count numbers should be retained in following conversion.
reformat.sh in=your.fq.gz out=your.fa
If these are pair-end reads then you should process them together with in1= and in2= directives and capture results in out1= and out2=. Only those reads where R1/R2 are identical would be considered duplicates. Remember to use addcount=t subs=0. Depending on size of your data files clumpify.sh can need a significant amount of memory.
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Are you sure you know what are you asking? That sounds like you want to extract unique reads and then count them. Please explain what do you want to do and if you have specific questions.