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Can I use sorted bam files from STAR with Stringtie?

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
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updated by Ram Ram • written by dina.hesham139 dina.hesham139

Thank you a lot!!

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

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written by dina.hesham139 dina.hesham139

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.

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updated by Ram Ram • written by Amitm Amitm

1 answer

hi,

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

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updated by Ram Ram • written by Amitm Amitm

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