Cuffdiff - Error in running cuffdiff by using the merged transcriptome assembly along with the BAM files from TopHat
0
0
Entering edit mode
21 months ago
evashan96 • 0

Hi I'm new to RNA-Seq analysis. I ran the following command with cuffdiff: cuffdiff -o /home/silicon/mouse/diff_out -b /home/silicon/mouse/GRCm38/Sequence/Bowtie2Index/genome.fa -p 7 -L g1,g2 -u /home/silicon/mouse/assembly/merged_asm/merged.gtf, \ .//home/silicon/mouse/alignment/Tophat_S2/accepted_hits.bam, /home/silicon/mouse/alignment/samp12_alignment/accepted_hits.bam

and I got the following error: Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu). Error: cannot open reference GTF file /home/silicon/mouse/assembly/merged_asm/merged.gtf, for reading

Can anyone help me out?

rna-seq • 453 views
ADD COMMENT
0
Entering edit mode
ADD REPLY
0
Entering edit mode

Try this if you have one control and one treated sample cufflinks-2.2.1.Linux_x86_64/cuffdiff -u -p 25 --library-type fr-firststrand -o /Cuffdiff/Control_VS_Treated /Cuffmerge/merged.gtf Control/A_Sorted.bam Treated/C_Sorted.bam, -L Control,Treated

In case of replicates try the following command (replicates should be comma separated) cufflinks-2.2.1.Linux_x86_64/cuffdiff -u -p 25 --library-type fr-firststrand -o /Cuffdiff/Control_VS_Treated /Cuffmerge/merged.gtf Control/A_Sorted.bam,Control_2/A1_Sorted.bam Treated/C_Sorted.bam,Treated_2/C1_Sorted.bam -L Control,Treated Also check the location of your merged gtf file (cuffmerge output)

ADD REPLY

Login before adding your answer.

Traffic: 2676 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6