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  • Cufflinks 2 annotation possible after cuffdiff?

    Dear all,

    I'm currently performing an RNAseq analysis and used the most recent releases of the tuxedo pipeline to do so (bowtie2, tophat2, cufflinks2).

    After figuring out that the .bam files need to be sorted regardless of the aligner, I used the following command to run cufflinks on my aligned samples:

    nice cufflinks --GTF ./UCSC_annotation_hg19.gtf -p 8 -o ./sample_1_annotation ./sample_1_mapping/accepted_hits.bam.sorted.bam

    As can be seen, I provided an annotation in gtf format. Nevertheless, when I inspect the results of the whole cufflinks pipeline (including cuffmerge and cuffdiff) via cummerbund, my transcripts have no gene annotation besides the cufflinks internal XLOC identifiers.

    Does anyone have an explanation for this? And is it possible to annotate the transcripts AFTER running cuffdiff? I have a serious time issue at the moment, so I need to have at least something to show (the infamous "list of genes" for the bosses' big meetings...)

    Best regards

  • #2
    Solved

    Nevermind, I found a very simple solution as the genes.fpkm_tracking file contains XLOC identifiers as well as gene names provided from the annotation.

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