Hi SRA team, I have a question of how to check the integrity of the BAM or FASTQ files. The .sra.vdbcache files were downloaded using prefetch and validated using vdb-validate. But how can I check whether the extraction of BAM or FASTQ files from .vdbcache was complete and did not ...
the reads are written into the *_1.fastq and *_2.fastq files. Unmated reads are placed in *.fastq. If the accession has no spots with one single read, the *.fastq-file will not be created.
The toolbox provides several built-in blocks that perform specific tasks, such as filtering genomic reads or mapping reads to a reference genome. In addition, you can also convert any custom function into a block that you can use in your analysis pipeline. Using a combination of built-in ...
SRA files will be written to: $HOME/ncbi/public/sra/ # - If your HOME dir is constrained in space, make a symlink: # ln -s /dir_with_lots_of_free_space/ncbi ${HOME}/ncbi prefetch -v -t fasp SRR5353377 # Convert SRA file to gzipped FASTQ files with fastq-dump (SRA toolkit)....
4. FASTQ/FASTA concatenated The spots are not split : 4 lines of FASTQ or 2 lines of FASTA are written into one output-file for each spot. This mode allows for the output to be redirected to stdout via: '--stdout ( -Z )'.
SRA files will be written to: $HOME/ncbi/public/sra/ # - If your HOME dir is constrained in space, make a symlink: # ln -s /dir_with_lots_of_free_space/ncbi ${HOME}/ncbi prefetch -v -t fasp SRR5353377 # Convert SRA file to gzipped FASTQ files with fastq-dump (SRA toolkit)....