Question: How to identify the SiRNA abundance from transcriptome data
gravatar for akilabioinfo
15 months ago by
akilabioinfo0 wrote:

Hi all,

I am having transcriptome data of c.elegans i would like to analyse the differential expression of siRNA between wild and mutant type. Is it possible to identify the siRNA using this data?

I have followed the below protocol, Is it correct?

After preprocessing the fastq file i have performed the alignment using HISAT2 with c.elegans mRNA and ncRNA (ncRNA-does not include the siRNA)

I have filtered the unmapped reads and i converted the bam file to fastq file. (because siRNA sequences have not been annotated)

I have filtered the fastq file using following criteria, ( I am looking into G-siRNA with 22 nucleotide length) Reads should start with G Read length 22

I have used salmon/sailfish for quantification using annotated GTF

DESEQ2 for differential analysis

Using this procedure we obtained 25 genes are differentially expressed. but i am not sure about whether these reads belongs to siRNA or it is a piece of coding region.

Please help me to identify the siRNA from transcriptome data.

Looking forward for the reply.

Thanks with Regards, Akila Ranjith, Research Scholar, Department of Biotechnology, Indian Institute of Technology - Madras.

sirna galaxy rna-seq • 414 views
ADD COMMENTlink modified 15 months ago • written 15 months ago by akilabioinfo0
gravatar for Jennifer Hillman Jackson
15 months ago by
United States
Jennifer Hillman Jackson25k wrote:


This is the protocol in use? Differential abundance testing of small RNAs

If so, the results represent the siRNA abundance/differential expression.

Hope this helps! Jen, Galaxy team

ADD COMMENTlink written 15 months ago by Jennifer Hillman Jackson25k
gravatar for akilabioinfo
15 months ago by
akilabioinfo0 wrote:

Dear Jen,

 Thanks for the link. If we have small RNA sequence then only we can use this protocol. But my data belongs to transcriptome which also includes small RNA in that case how to extract the siRNA from the pool of transcriptome. can we use the same protocol in that case?

Thanks, Akila Ranjith

ADD COMMENTlink written 15 months ago by akilabioinfo0
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