blasting unaligned reads on usegalaxy
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3.4 years ago

Hello

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?

usegalaxy RNA-Seq hisat2 • 729 views
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You could try converting them to fasta, e.g. with the seqtk_seq tool.

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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.

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