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Post alignment QC parameters

Hello,

I am using human transcriptome as a reference for RNA-Seq data. I am done with the alignment of all the samples. For the post-alignment QC, I am aware RSeQC is widely used. However, almost all the parameters require the gene annotation file for that. Since I used transcriptome as a reference I did not use gene annotation gtf file. I am wondering what are the after alignment QC parameters I should test? and using which tool in this particular case.

Thank you in advance.

rna-seq rseqc
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updated by Brian Bushnell Brian Bushnell • written by KVC_bioinfo KVC_bioinfo

If you really want suggestions, please be more specific about what you did: which transcriptome did you used? Which program and command-line did you use for the alignment?

You may try the BAM QC module from QualiMap.

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written by h.mon h.mon

Thank you. As mentioned I used human transcriptome as a reference for RNA-seq samples. and while using RseQC I was not sure what annotation file I should use. I resolved my problem. I downloaded the gtf file from the UCSC table browser.

Thanks.

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written by KVC_bioinfo KVC_bioinfo

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