Question: Running Cufflinks and transcriptome.gtf is empty (i.e. 0 bytes and no characters)
gravatar for delods0
4.5 years ago by
United States
delods00 wrote:

Hi all,


I have been working on building a transcriptome for HAdV5. My process has been as follows:


1) use bowtie2-build to make HAdV reference genome index

2) map reads of HeLA infected cells (found online) using Tophat2 (gene annotated file was also found online, so I used --transcriptome-index option).

3) use Cufflinks on the generated accepted_reads.bam file 

Now I'm pretty sure that steps 1 and 2 have been done correctly and that the formatting etc is all correct. The problem I have is that after running cufflinks, my transcripts.gtf file is 0 bytes and is blank. The other files produced are there but are extremely small and do not contain much in them (maybe a line or two). I don't get any errors when running Cufflinks so I'm wondering if anyone has some incite on what is going on? The command I used in cufflinks was: cufflinks -p 3 -o cuff_all accepted_reads.bam (note that accepted_reads.bam is in the same file as all the other files I have created and used in my attempt to make this transcriptome). 


Let me know if you need any additional information, thanks!

ADD COMMENTlink written 4.5 years ago by delods00
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1181 users visited in the last hour