Hi all,
be gentle with me - its my first post! I have two conditions with 3 replicate files.
Ive run tophat and cufflinks successfully on the RNAseq data.
However when it comes to merging the gtf transcripts, despite following the nature protocol closely, cuffmerge is not running properly.
Ive seen a few people post this question in different forums but I haven't seen anyone answer the query so I dont know what the solution is!
Essentially after running the cuffmerge command on a compiled assemblies script file list, it looks like the operation is starting but after about 10 seconds I get returned to the command prompt. No error messages appear but the merged asm folder is empty and the program has clearly aborted. I just dont know why .
Can anyone please help? Im running linux on an ubuntu parallels system with 12GB memory allocated. The bin folder contains symbolic links to the bowtie2 genome files and the gtf gene file. Thanks again if anyone can point me to things to check! Apologies in advance for any forum rules I have probably broken!
be gentle with me - its my first post! I have two conditions with 3 replicate files.
Ive run tophat and cufflinks successfully on the RNAseq data.
However when it comes to merging the gtf transcripts, despite following the nature protocol closely, cuffmerge is not running properly.
Ive seen a few people post this question in different forums but I haven't seen anyone answer the query so I dont know what the solution is!
Essentially after running the cuffmerge command on a compiled assemblies script file list, it looks like the operation is starting but after about 10 seconds I get returned to the command prompt. No error messages appear but the merged asm folder is empty and the program has clearly aborted. I just dont know why .
Can anyone please help? Im running linux on an ubuntu parallels system with 12GB memory allocated. The bin folder contains symbolic links to the bowtie2 genome files and the gtf gene file. Thanks again if anyone can point me to things to check! Apologies in advance for any forum rules I have probably broken!
$ cuffmerge -g genes.gtf -s genome.fa -p 4 assemblies.txt
[Wed Oct 7 03:01:46 2015] Beginning transcriptome assembly merge
-------------------------------------------
[Wed Oct 7 03:01:46 2015] Preparing output location ./merged_asm/
[Wed Oct 7 03:02:23 2015] Converting GTF files to SAM
j12@ubuntu:~/bin$
[Wed Oct 7 03:01:46 2015] Beginning transcriptome assembly merge
-------------------------------------------
[Wed Oct 7 03:01:46 2015] Preparing output location ./merged_asm/
[Wed Oct 7 03:02:23 2015] Converting GTF files to SAM
j12@ubuntu:~/bin$
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