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Question: Hisat2 to cufflinks
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gravatar for garentguuu
6 months ago by
garentguuu • 10
garentguuu • 10 wrote:

Hi,

Recently, I tried use hisat2 to mapping RNA-seq, then use cufflinks to measure the gene expression in galaxy. I am curious about the step after hisat2. If I finished hisat2, should I need use to samtools to sort the bam file? Because I did not sort the output of hisat2, and it run well in cufflinks. I am curious about the result, it is right or not, compared with sorted bam in galaxy?

Thanks! Garen
rna-seq cufflinks galaxy • 611 views
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modified 6 months ago by Jennifer Hillman Jackson ♦ 25k • written 6 months ago by garentguuu • 10
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gravatar for Jennifer Hillman Jackson
6 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

HISAT2 will already produce a coordinate sorted BAM output, so no need to re-sort.

You might have already found this tutorial, or know the usage, but just to add a bit of info: make sure that you are using HISAT's reporting options for Cufflinks. This is how: https://galaxyproject.org/tutorials/nt_rnaseq/#spliced-mapping-with-hisat

Thanks! Jen, Galaxy team
ADD COMMENT • link written 6 months ago by Jennifer Hillman Jackson ♦ 25k
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