Question: SRA data sets and runs
0
gravatar for MAPK
12 months ago by
MAPK1.3k
United States
MAPK1.3k wrote:

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.

sra rnaseq • 610 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by MAPK1.3k
2
gravatar for genomax
12 months ago by
genomax58k
United States
genomax58k wrote:

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

ADD COMMENTlink written 12 months ago by genomax58k

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

ADD REPLYlink written 12 months ago by MAPK1.3k
2
gravatar for mforde84
12 months ago by
mforde841.2k
mforde841.2k wrote:

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.

ADD COMMENTlink written 12 months ago by mforde841.2k

Thanks to both of you

ADD REPLYlink written 12 months ago by MAPK1.3k
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