hi Everyone,
I am new in RNAseq analysis. I have run tophat then cufflinks, and now I wnat to run cuffmerge, but I have found this problem:
# cuffmerge -p 4 -g /path/to/genes.gtf -s /path/to/genome.fa /path/to/assemblies.txt
[Thu Oct 23 13:18:51 2014] Beginning transcriptome assembly merge
-------------------------------------------
[Thu Oct 23 13:18:51 2014] Preparing output location ./merged_asm/
Traceback (most recent call last):
File "/usr/bin/cuffmerge", line 580, in <module>
sys.exit(main())
File "/usr/bin/cuffmerge", line 530, in main
transfrag_list_file = open(args[0], "r")
IOError: [Errno 2] No such file or directory: '/home/michalina/BAM_SAM_tophat_samtools/TS2/assemblies.txt
I have no idea what is going wrong. My cufflinks were wrong? gtf or fa references file are not appropriate? hese are the same reference files that I use for previous analysis (tophat, cufflinks).
many thanks for any commnet or advise
M.
I am new in RNAseq analysis. I have run tophat then cufflinks, and now I wnat to run cuffmerge, but I have found this problem:
# cuffmerge -p 4 -g /path/to/genes.gtf -s /path/to/genome.fa /path/to/assemblies.txt
[Thu Oct 23 13:18:51 2014] Beginning transcriptome assembly merge
-------------------------------------------
[Thu Oct 23 13:18:51 2014] Preparing output location ./merged_asm/
Traceback (most recent call last):
File "/usr/bin/cuffmerge", line 580, in <module>
sys.exit(main())
File "/usr/bin/cuffmerge", line 530, in main
transfrag_list_file = open(args[0], "r")
IOError: [Errno 2] No such file or directory: '/home/michalina/BAM_SAM_tophat_samtools/TS2/assemblies.txt
I have no idea what is going wrong. My cufflinks were wrong? gtf or fa references file are not appropriate? hese are the same reference files that I use for previous analysis (tophat, cufflinks).
many thanks for any commnet or advise
M.
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