Question: RNA-SeQC does not calculate information about "Strand Specificity"
gravatar for Lina F
13 days ago by
Lina F50
Boston, MA
Lina F50 wrote:

Hi all,

I recently ran RNA-SeQC on yeast RNAseq data to assess the quality of the sequencing run.

Unfortunately, the tool returned only "NA" for the "Strand Specificity" section:


This sample contains single-end reads that I mapped to the reference using STAR using the following command:

$> ~/STAR --runThreadN 20 --genomeDir ./yeast_index --outFileNamePrefix ./star_out --readFilesIn sample_10-b-8.fastq --limitBAMsortRAM 1207105173 --outSAMtype BAM SortedByCoordinate --outSAMattrRGline ID:HWLCLBGXZ_1_17 SM:Sample_10-b-8

Are there any other options I need to set in STAR to provide strand specificity information?

Thanks for any suggestions!

rna-seq qc • 106 views
ADD COMMENTlink modified 13 days ago by Charles Warden4.6k • written 13 days ago by Lina F50
gravatar for Charles Warden
13 days ago by
Charles Warden4.6k
Duarte, CA
Charles Warden4.6k wrote:

You can see, is strand-specific? for more information about getting strand-specific information from RSeQC via I'm not familiar with the report format that you provided, but I know that works. You can also double-check that chromosome format for the gene annotations matches the chromosome format of your alignment.

You don't have to specify a parameter for the strand for the STAR alignment, but you could use some or all of the following strategies to affect your splice junctions:

1) You can add --outSAMstrandField intronMotif to add a strand attribute, which might be needed for some downstream analysis

2) You can use a --twopassMode Basic setting to refine alignments around junctions

3) You can provide genomic annotations when creating your indexed reference (and there are parameters to specify a splice junction database during alignment)

ADD COMMENTlink modified 13 days ago • written 13 days ago by Charles Warden4.6k

Thanks for the suggestion!

I am actually using the RNA-SeQC tool from the Broad Institute; that's where the report came from. I will take a look at the tool you mentioned, maybe it will be more appropriate.

ADD REPLYlink written 13 days ago by Lina F50
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1505 users visited in the last hour