Evaluation of RSeQC report

Question

[fawazfebin]

Hi

I was doing a quality check of bam file output of STAR alignment in RNASeq analysis. I selected RSeQC for the same and here I paste the output of bam_stat.py command:

#=========================================
# All numbers are READ count
#=========================================
Total records:                          37463450

QC failed:                              0
Optical/PCR duplicate:                  0
Non primary hits                        9558982
Unmapped reads:                         0
mapq < mapq_cut (non-unique):           4344540

mapq >= mapq_cut (unique):              23559928
Read-1:                                 0
Read-2:                                 0
Reads map to '+':                       11778663
Reads map to '-':                       11781265
Non-splice reads:                       19519751
Splice reads:                           4040177
Reads mapped in proper pairs:           0
Proper-paired reads map to different chrom:0

How do I evaluate the quality of the alignment from the above report ? Kindly guide.

[fawazfebin]

Is it OK to proceed with the Differential Expression step?

[Kevin Blighe]

Hey fawaz, can you tidy the formatting of your post? At the moment, the terms and numbers are 'all over the place', and it may discourage others from responding.

Thanks!

Kevin

[Kevin Blighe]

I think that my colleague has edited it for you. The output looks normal apart from:

Read-1: 0

Read-2: 0

...

Reads mapped in proper pairs: 0

Just also check the output of samtools flagstat on your BAM file (see here: What Does Samtools Flagstat Results Mean? ).

[fawazfebin]

Thank you Kevin. I shall have a look at samtools flagstat. And thanks for the edit too.