I am analysing both sRNA data and mRNA data for differential expression from bacteria. For mRNA-seq I used the pipeline Bowtie+Stringtie+Ballgown. For sRNA i am planning to use, Bowtie+HTseq-count+DESeq2. I opted for HTseq2 + DEseq2 as I didnt find any previous references that have used STRINGTIE for small RNAs. Which one is a better option? will using STRINGTIE give more accurate results than HTseq+DESeq2?
I was wondering what sRNA means but I suppose these are small RNA-Seq reads to find small non codingRNAs? For small RNA's I would not use Stringtie as assembler - it tries to assemble genes and their intron exon structure and thats not what you will be sequencing with small RNA-Seq. In small RNA-Seq you will be sequencing miRNAs and other ncRNA derived fragments up to a size of ~35bp. If do you want to find miRNAs, you could go for tools like miRDeep but those are highly specific for miRNAs only. If you want to use a small ncRNA assembler that shouldn't give any bias towards a certain sub type of small ncRNAs you could go for BlockBuster or (okay, this will obviously be biassed as I wrote the tool myself) FlaiMapper which I believe works better, in particular, for snoRNAs. I am rewriting that package to make it compatible with entire reference genomes so you could use it on bacteria as well. This will be finished somewhere this or next week..
After assembly it is fine to use HTseq-count+DESeq2 if you like to. EdgeR and/or featureCounts will be fine too - it doens't matter too much which of those you use.
I gave a talk on small RNA-Seq two days ago. You can have a look if you're interested:
Thank you for your detailed answer. Infact I am doing non-coding RNA's in bacteria, and currently focus only on the differential expression and not on identification of novel sRNA's (That part was done earlier by another team and I am using their annotation for my works).