SRA data sets and runs

Question

[MAPK]

Hi All, I am looking at this RNA-seq data here. I want to know which specific run do I need to select from as there are 36 different runs starting from SRR id SRR3285884 to SRR3285919. I want to assemble this specific transcriptome data using Trinity for my research and I am not sure which run I should be selecting. Please clarify. Another question I have is about trimming- since the Design description (copied below) from the link above states that the mRNA were selected using poly-T containing beads, Do I need to do the trimming of poly-T/A tails before assembly? Thank you.

Design: RNA-seq libraries have been prepared according to Illumina’s protocols using the Illumina TruSeq RNA sample prep kit to analyze mRNA v2 (P.N. RS-122-2001) to analyze mRNA. mRNA were selected using poly-T containing beads to remove other RNA. Then, RNA were fragmented to generate double stranded cDNA to be sequenced.

Answer 1

[GenoMax]

You may need to get all of them. Just follow standard scan/trim procedures you have used in past.

[MAPK]

Is it ok if I merge all fastq files extracted from these 36 runs of SRA files and do a single analysis?

Answer 2

[mforde84]

Looks like there are multiple sequencing runs for the species. So you should probably use all of them. Also, you don't really have to worry about polyA, as the library is size selected. Trimming is typically done to remove any adapter contamination at the beginning or the end of the read. Unless your alignments are crap, or the pre alignment QC indicated alot of adapter contamination, then I wouldn't worry about it.

[MAPK]

Thanks to both of you