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Dear All,

I am trying to measure the expression values ( in RPKM ) for gencode lncRNA uploaded in your site, using flux capacitor. But it shows RPKM 0.000 for all transcript.Can you please suggest a sample command in details?

I am using following command with no luck, all output RPKM is 0.000

sh flux-capacitor -i  myinput.bam  -a gencode.v12.annotation.patched_contigs.gtf  -o myoutput.txt --threads 2

Here is a sample output:

1  HAVANA    transcript    12010    13670    .    +    .    transcript_id "ENST00000450305.2"; locus_id "1:11869-14412W"; gene_id "ENSG00000223972.4"; reads 0.000000; length 632; RPKM 0.000000



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  1. Hi Tanvir,

    if you exclusively find 0-quantifications in your output, then something is oddly wrong between the provided reads and the annotation. Have a look at the stderr stream during the program run, the report should say that there was no read that maps to the provided annotation. From the name of your annotation file I guess that you may have modified some chromosome/contig names. It is possible that the reference sequence names between annotation and bam file are not the same (e.g., "chr9" in one and just "9" in the other one)? That could explain your observation.





    1. Hi Micha Sammeth,

      YES, you are right!  Chromosome name mismatched for bam/sam (e.g. chr1) and gff (e.g. 1) file. Thanks.

      And you didn't comment on command for  measuring expression value for a transcript: Can you please mention how to do for single and paired reads from terminal , not using parameter file. I run following command from terminal:

      sh flux-capacitor -i  myinput.bam  -a gencode.v12.annotation.patched_contigs.gtf  -o myoutput.txt --threads 2

      Is the above command right? how to mention single or pair end read from terminal ?