Question: Can I use sorted bam files from STAR with Stringtie?
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gravatar for dina.hesham139
3.1 years ago by
Egypt
dina.hesham139100 wrote:

Hey,

I mapped my fastq files using STAR. The output now is a sorted bam files. I wanted to try Stringtie instead of cufflinks.

But since my output doesn't contain the tag XS, Can Stringtie deal with it ?

 

Thank you!

rna-seq assembly • 2.2k views
ADD COMMENTlink modified 3.1 years ago by Amitm1.6k • written 3.1 years ago by dina.hesham139100
0
gravatar for Amitm
3.1 years ago by
Amitm1.6k
UK
Amitm1.6k wrote:

hi,

STAR has the provision of returning the XS attribute with the --outSAMstrandField parameter.

ADD COMMENTlink written 3.1 years ago by Amitm1.6k
0
gravatar for dina.hesham139
3.1 years ago by
Egypt
dina.hesham139100 wrote:

Thank you a lot!!

Okay. What if I already mapped without this option, can I still use Stringtie?

ADD COMMENTlink written 3.1 years ago by dina.hesham139100
0
gravatar for Amitm
3.1 years ago by
Amitm1.6k
UK
Amitm1.6k wrote:

hi,

From StringTie Manual page -

"

Every spliced read alignment (i.e. an alignment across at least one junction) in the input SAM file must contain the tag XS to indicate the genomic strand that produced the RNA from which the read was sequenced. Alignments produced by TopHat and HISAT2 (when ran with --dta option) already include this tag, but if you use a different read mapper you should check that this XS tag is included for spliced alignments

"

So, you would need to redo if you want to use StringTie or Cufflinks.

ADD COMMENTlink written 3.1 years ago by Amitm1.6k
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