Question: BLAST stranded SRA for plus or minus?
1
gravatar for Adria
12 months ago by
Adria10
Switzerland
Adria10 wrote:

I'm trying to look into existing RNAseq datasets to see if my highly expressed gene of interest may have both plus and minus strands expressed. There are a pack of SRA datasets that are strand specific. I know that I can blast them (SRA nblast), but when I blast the known mRNA and the reverse complement I get the same pattern.

Any tips/tricks to get at this?

blast rna-seq sra • 494 views
ADD COMMENTlink modified 11 months ago by h.mon21k • written 12 months ago by Adria10
0
gravatar for h.mon
11 months ago by
h.mon21k
Brazil
h.mon21k wrote:

Map the SRA datasets with STAR to the appropriate annotated reference genome and using the --quantMode GeneCounts parameter. With this parameter, STAR will output gene counts for all strandedness options:

column 1: gene ID

column 2: counts for unstranded RNA-seq

column 3: counts for the 1st read strand aligned with RNA (htseq-count option -s yes)

column 4: counts for the 2nd read strand aligned with RNA (htseq-count option -s reverse)

Then you can:

  1. check the quality of strand-specificity with RSeQC infer-experiment-py
  2. look at your gene of interest counts
  3. view the bam mapping files with IGV
ADD COMMENTlink written 11 months ago by h.mon21k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1047 users visited in the last hour