Question: Cuffdiff Error: Cuffdiff Requires At Least 2 Sam Files
gravatar for Lisanne
7.2 years ago by
Lisanne20 wrote:

Dear All,

I am really confused about the cuffdiff function in cufflinks. I thought that cuffdiff needs at least to BAM or SAM files. I have 2 accepted_hits.sam files and one combined_transcripts.gtf. I try this:

cuffdiff -o A1_A3 -q A1_A2.combined.gtf A1/A1_accepted_hits.sam A3/A3_acctepted_hits.sam ERROR: cuffdiff requires at least 2 SAM files

And for the BAM files: cuffdiff -o A1_A3 -q A1_A2.combined.gtf A1/A1_accepted_hits.bam A3/A3_acctepted_hits.bam ERROR: cuffdiff requires at least 2 SAM files

Can anyone please tell me what I am doing wrong? Thanks!

cufflinks cuffdiff error • 6.7k views
ADD COMMENTlink modified 5.2 years ago by Biostar ♦♦ 20 • written 7.2 years ago by Lisanne20
gravatar for Dinesh Cyanam
7.2 years ago by
Ann Arbor, MI
Dinesh Cyanam10 wrote:

Hi, I believe you are receiving the error because you misspelled accepted in your A3 file. The file name should be A3_accepted_hits.sam

Also, make sure that the GTFs and the SAM and BAM files are in the given path and I would use the combined GTF of sample A1 and A3 and not A1 and A2 as you mentioned above.

ADD COMMENTlink written 7.2 years ago by Dinesh Cyanam10
gravatar for Sta
7.1 years ago by
Sta0 wrote:

i have the same prblem with my data.

I use the command:

cuffdiff - diffout -b /home/thx/genome.fa -p 8 -L /home/sta/Gen/accepted_hits.bam /home/sta/Gen2/accepted_hits.bam -u /home/sta/gtf/mm9.gtf

ERROR: cuffdiff requires at least 2 SAM files

but... if i try 2 convert bam into sam it is also not working!

Command here: samtools view -bt /home/sta/index/mm9.fa accepted_hits.sam

Can anyone help here?

ADD COMMENTlink written 7.1 years ago by Sta0

i use version 1.3.0

ADD REPLYlink written 7.1 years ago by Sta0
gravatar for Bontus
7.0 years ago by
Bontus80 wrote:

@STA: Given the information in the manual

you use the flag for labelling groups -L without specifying any group labels in this command: cuffdiff - diffout -b /home/thx/genome.fa -p 8 -L /home/sta/Gen/accepted_hits.bam /home/sta/Gen2/accepted_hits.bam -u /home/sta/gtf/mm9.gtf

for using labels, try: cuffdiff -o diffout -b /home/thx/genome.fa -p 8 -L C1,C2 -u /home/sta/gtf/mm9.gtf /home/sta/Gen/accepted_hits.bam /home/sta/Gen2/accepted_hits.bam

or without: cuffdiff -o diffout -b /home/thx/genome.fa -p 8 -u /home/sta/gtf/mm9.gtf /home/sta/Gen/accepted_hits.bam /home/sta/Gen2/accepted_hits.bam

ADD COMMENTlink written 7.0 years ago by Bontus80

I am also facing a similar issue. My command is as follows:

cuffdiff -p 6 -o ./UM108_cuffdiff -u --compatible-hits-norm -M Homo_sapiens.GRCh37.75.gtf \ 61327_tophat.bam \ 61328_tophat.bam

I also tried the same command as a single line and I still get this error - "Error: cuffdiff requires at least 2 SAM files"

Could someone please help me out with this ?

Thanks, Aditi

ADD REPLYlink written 2.6 years ago by aditisk0
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