RawAlign - d3_yeast_r94
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下载链接：
https://zenodo.org/record/8417882
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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:
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
创建时间：
2023-10-08
