RawAlign - d3_yeast_r94
收藏资源简介：
FASTA files extracted from FAST5 files from the following NCBI link: https://trace.ncbi.nlm.nih.gov/Traces/index.html?view=run_browser&acc=SRR8648503&display=metadata The reads are extracted using the "Fast5-to-Fastq" tool (https://github.com/rrwick/Fast5-to-Fastq) with the following commands: <pre><code class="language-bash">wget -qO- https://sra-pub-src-1.s3.amazonaws.com/SRR8648503/GLU1II_basecalled_fast5_1.tar.gz.1 | tar -xzv; find ./GLU1II_basecalled_fast5_1 -type f -name '*.fast5' | head -50000 | xargs -i{} mv {} ./fast5_files/; rm -rf GLU1II_basecalled_fast5_1; #To extract the reads from FAST5 from this dataset, you will need to clone the following repository and make sure you have h5py <= 2.9 (if you have conda you can do the following): conda create -n oldh5 h5py=2.9.0; conda activate oldh5; git clone https://github.com/rrwick/Fast5-to-Fastq Fast5-to-Fastq/fast5_to_fastq.py fast5_files/ | awk 'BEGIN{line = 0}{line++; if(line %4 == 1){print ">"substr($1,2,36)}else if(line % 4 == 2){print $0}}' > reads.fasta</code></pre>
