Question: How to obtain unspliced tRNAs from FASTQ file
0
gravatar for nkabo
8 weeks ago by
nkabo50
nkabo50 wrote:

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.

ADD COMMENTlink modified 17 days ago • written 8 weeks ago by nkabo50
3

theoretically it might be possible (see swbarnes2 answer on how), but :

  • RNAseq is usually processed RNA which means it is in most cases already spliced (unspliced reads are rather an exceptions/artefact)
  • dependant on the type of RNA data you have, you should check how the RNA libraries were constructed as most often (default bulk rna-seq) is poly-A captured, meaning it is focussed on mRNA molecules and would thus omit most of the other RNA types
ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by lieven.sterck9.5k

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!

ADD REPLYlink modified 17 days ago • written 17 days ago by nkabo50
2
gravatar for swbarnes2
8 weeks ago by
swbarnes29.4k
United States
swbarnes29.4k wrote:

Here's what I'd try:

1) Find sequences of unspliced tRNA genes, make a reference fasta

2) Align your fastqs to that reference.

ADD COMMENTlink written 8 weeks ago by swbarnes29.4k

Thank you for your reply, I will try this approach. I think , after obtaining sequences for unspliced tRNA genes, I need to align the unprocessed version of RNAseq to these unspliced tRNA genes; since such small genes could be eliminated during the processing as lieven.sterck mentioned. I am looking for a source for unspliced tRNA genes, but I am not quite sure how I could detect unspliced tRNA genes and get their sequences. Could you suggest me a source for such aim? Thanks in advance.

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by nkabo50
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