Analysis of non-templated residues

I would like to perform an analysis of non-templated adenosine residues added to the end of RNAs in bacteria. In bacteria poly(A) sequences, if they are present, are generally quite short. What tools could I use to identify the location and length distribution of such non-templated residues using RNA-seq data?

Hi @cjain
I guess it depends on data and information you have. Maybe find a paper describing a similar analysis and follow the protocol.
Kind regards,
Igor

Thanks!. I did find some papers (e.g., PMID 35524564), but am not sure how to apply the methods described in the paper using Galaxy.

Regards,

cjain

Hi @cjain
from a quick look, public Galaxy servers have tools used in the paper: bowtie1 (Map with Bowtie for Illumina), cutadapt, trimming tool from fastx (Trim sequences)., SAMtools, bedtools.
Kind regards,
Igor

Thank you for your suggestions. I will take a look at the tools you suggested.

On another note, I wonder if you can suggest any tools to analyze deletion mutation frequencies in CLIP data? Cross-linking of proteins with RNA followed by reverse transcription sometimes leads to deletion mutations and one can use that information to identify precise interaction sites. I have used Samtools mpileup and Naive Variant Caller for analyzing single-nucleotide variants but could not figure out how to get information on deletions.

Thank you,

cjain

hi @cjain
Unfortunately, I am not familiar with CLIP analysis.
Indels can be called with bcftools mpileup or FreeBayes. I have not used Naive Variant Caller for some itme, and I don’t remember if it is suitable for indels.
Kind regards,
Igor