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How do you convert FASTQ to fast5?
fast5 is a variant of HDF5 the native format in which raw data from Oxford Nanopore MinION are provided. You can easily extract the reads in fast5 format into a standard fastq format, using for example poretools . Say I have aligned these reads in fastq format to an external reference genome, resulting in a SAM file.
Can you convert FASTQ to fasta?
Fastq is currently the most common file-format for unassembled sequence reads and you’ll loose all base quality information when converting it to fasta. Depending on what you are planning to do, you may not have to convert it.
Can you blast a FASTQ file?
You can’t use a fastq format file to do blast.
What is fast5 file?
The FAST5 format is the standard sequencing output for Oxford Nanopore sequencers such as the MinION. It is based on the hierarchical data format HDF5 format which enables storage of large and comples data. In contrast to fasta and fastq files a FAST5 file is binary and can not be opened with a normal text editor.
What is magic blast?
Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of RNA-seq, locating the candidate introns and adding up the score of all exons.
Which is the best tool to convert Fast5 to FASTQ?
Albacore (Oxford Nanopore’s basecaller) can basecall directly to FASTQ, which makes FAST5 to FASTQ conversion much less relevant.
Can a.fastq file work as a input format?
Both *.fastq and *.fastq.gz should work as input formats. I ran into some annoying crashes caused by corrupt FAST5 files, so I made the fast5_integrity_check.py tool to find these.
How is FASTQ compressed in GZ to FASTA?
FASTQ Compressed in gz to FASTA gzip is used to uncompress the FASTQ file and awk to parse the FASTQ into FASTA: 1.2. FASTQ to FASTA cat is used to stream data the FASTQ file and awk to parse the FASTQ into FASTA:
How to subset reads from the Fast5 archive?
With the read ID, I can then grep them out from the file containing the reads in fastq format, generating a subset file in fastq format containing only the IDs that have mapped to the reference. Now my question is, can we subset reads from the fast5 archive according to the list of mapping reads as taken from the file with reads in fastq format?