how to use Cufflinks to detect junction

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4.9 years ago

zhao03 ▴ 70

can the cufflinks be used to discover splice junction ? OR other tools can obtain splice junctions? thank you for your answer!

RNA-Seq rna-seq next-gen assembly • 1.2k views

ADD COMMENT • link 4.9 years ago by zhao03 ▴ 70

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i want to obtain splice junctions based on mapping result of STAR

ADD REPLY • link 4.9 years ago by zhao03 ▴ 70

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is one of the output files from STAR not a junction file?

ADD REPLY • link updated 4.9 years ago by Ram 43k • written 4.9 years ago by lieven.sterck 15k

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thanks, I apologized for not being able to clearly describe my problem. yes, there is a file sorted junctions called SJ.out.tab, however, most papers i read used bam file to extract junctions , and two popular tools for isoform quantification, MISO and Cufflinks(ref: Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data). Do you have any suggestions?

ADD REPLY • link 4.9 years ago by zhao03 ▴ 70

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thanks however, your question still a little unclear to me. Do you now want a BAM output or look for splice junctions?

ADD REPLY • link 4.9 years ago by lieven.sterck 15k

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thank you. In fact , i want to extract splice junctions using difference methods, including from BAM file.

ADD REPLY • link 4.9 years ago by zhao03 ▴ 70

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