Hi,
I want to align the fastq file onto genome using blasr, however, blasr only accept fasta or bax.h5 file format. fastq does not contain the quality information. So is it possible to convert the fastq file to bax.h5 file format?
Actually, I have sequenced a PacBio transcriptome. There is many raw subreads have not been utilized at clustering step of IsoSeq pipeline. So I want to align the remain subreads onto the genome to have a check the quality of alignment and alignment ratio. BLAT also can do this job. To compare with BLAT, I also want to test blasr. So If I want to do this work, I have two choice:
- convert fastq to bax.h5 format
- extract the remain subreads from the original bax.h5 file.
For choice 2, the bax.h5 file is big than fastq, and further how to extract subsection of this file into bax.h5 format?
Best,
Pengcheng
Hi Daniel,
Thank you for your reply and the information. I indeed checked the help information after I installed blasr. But not read the README.md file. Sorry, I will have a try.