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  • bvk
    replied
    Originally posted by GenoMax View Post
    No. That is not correct.

    -L has to be a comma separated list of condition labels.

    -L cond1,cond2 (e.g. -L Control,Mutant)

    Your list of bam files (comma delimited names no spaces, then two conditions separated by a space) will be. e.g. cond1.bam1,cond1.bam2,cond1.bam3 (space here) cond2.bam1,cond2.bam2,cond2.bam3
    You missed it. please, see it after 3rd bam file I haven't given any comma. And it is separated with space too.

    Leave a comment:


  • GenoMax
    replied
    No. That is not correct.

    -L has to be a comma separated list of condition labels.

    -L cond1,cond2 (e.g. -L Control,Mutant)

    Your list of bam files (comma delimited names no spaces, then two conditions separated by a space) will be. e.g. cond1.bam1,cond1.bam2,cond1.bam3 (space here) cond2.bam1,cond2.bam2,cond2.bam3
    Last edited by GenoMax; 05-05-2015, 03:16 AM.

    Leave a comment:


  • bvk
    started a topic cuffdiff for groups

    cuffdiff for groups

    I want run cuffdiff for two groups. each has 3 samples. Is the below code right?

    cuffdiff -o diff_out -b ../genome/ce10.fa -p 2 -L em,la -u merged_asm/merged.gtf cond1.bam1,cond1.bam2,cond1.bam3 cond1.bam1,cond1.bam2,cond1.bam3
    Last edited by bvk; 05-05-2015, 05:33 AM.

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