Entering edit mode
2.3 years ago
demoraesdiogo2017 ▴ 90
Two of my samples had very low alignment percentage (44 and 32%). I asked HISAT2 to make separate files for unaligned reads which are on fastqsanger formats. I would like to BLAST these unaligned reads to have an idea where this contamination came from. I would like to use NCBI BLAST+ blastn on usegalaxy to do so. However, the unaligned reads (in fastqsanger format) that HISAT2 apparently are not suitable for this. I tried uncompressing these files, but still can't use them. Any suggestions?
You could try converting them to fasta, e.g. with the
Generally there is no need to blast every unaligned read. If you suspect there is contamination you could take a sample of reads (~10) and use web blast at NCBI. You should be able to view your data in galaxy and grab a set of reads. You can easily convert them to fasta format by changing
@beginning of fastq header to
>and then getting rid of the
+and the q-score string in lines 3 and 4 from fastq records.