how to use Cufflinks to detect junction

0

Entering edit mode

5.5 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 • 1.3k views

ADD COMMENT • link 5.5 years ago by zhao03 ▴ 70

0

Entering edit mode

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

ADD REPLY • link 5.5 years ago by zhao03 ▴ 70

0

Entering edit mode

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

ADD REPLY • link updated 5.5 years ago by Ram 44k • written 5.5 years ago by lieven.sterck 15k

0

Entering edit mode

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 5.5 years ago by zhao03 ▴ 70

0

Entering edit mode

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 5.5 years ago by lieven.sterck 15k

0

Entering edit mode

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

ADD REPLY • link 5.5 years ago by zhao03 ▴ 70

Login before adding your answer.