Dear all,
I have RNA-seq data coming from peripheral blood leukocytes. I have FASTQ file and I was asked to obtain unspliced tRNAs from that file. I am a beginner in RNA-Seq analysis and I do not know how I could extract unspliced tRNAs from FASTQ file. I tried to find a workflow or tool, but I could not detect any. I would like to ask:
- Is it possible to obtain unspliced tRNAs from a FASTQ file?
- If it is possible, could you suggest me a way/tool/workflow for such task?
Thanks in advance.
theoretically it might be possible (see swbarnes2 answer on how), but :
Dear community,
@swbarnes2 suggested me to obtain sequences of unspliced tRNA genes and do the aligning afterwards. However, I could find regular tRNA sequences to do the alignment, but I could not see any groups of sequences, specifically belonging to unspliced tRNAs. A colleague also suggested to use "misc" part in NCBI, but I could not quite catch how it could be used in this case.
Could you propose a way to find sequences of unspliced tRNA genes?
Thanks in advance!