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getzlab / rnaseqc

Fast, efficient RNA-Seq metrics for quality control and process optimization
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RNA-seQC output empty #46

Closed YyLu5 closed 4 years ago

YyLu5 commented 4 years ago

Hi,

I followed the TOPmed pipeline used STAR to get the bam file, picard to mark duplicate, then used RNA-seQC to generate gene tpm. All steps ran without any error, however the gene_tpm.gct file only contain nan for tpm column, and exon_reads.gct and other files contain only 0 for last column, the first two columns (ID and name) looks fine. head gene_tpm.gct

image

head exon_reads.gct image

Therefore I double checked my work, and noticed a warning from picard mark duplicate step, because the log is very long, I will only paste the head and tail here: image

image

Did this cause the empty output? I've been searching online for solution for several days and did not get any valid results. I tried both STAR BAM file and the BAM file after mark duplicates, both them gave the same results.

Software I used are STAR 2.7.3a, Picard v2.18.17 and rnaseqc.v2.3.6.linux.

Thank you for your help!

YyLu5 commented 4 years ago

Hi, I'm able to figure it out, the problem caused by my single ended data.