Question: cufflinks/cuffdiff command line
0
gravatar for dimitrischat
3.2 years ago by
dimitrischat110
dimitrischat110 wrote:

i ve been trying to figure out the command line for cufflinks/cuffdiff but i have been getting error again and again. Trying the command line with 2 bam files from tophat :

cuffdiff -p 2 --labels esred1,esred2 - b /Users/../mm9genome.fa  /Users/.../accepted_hits-red1.bam,/Users/.../accepted_hits-red2.bam
error(s) : number of labels must match number of conditions

cuffdiff -p 2 - b /Users/.../mm9genome.fa  /Users/.../accepted_hits-red1.bam,/Users/.../accepted_hits-red2.bam
error : cannot open reference GTF file - for reading

cuffdiff -p 2 - L esred1,esred2 - b /Users/.../mm9.fa  /Users/.../accepted_hits-red1.bam,/Users/.../accepted_hits-red2.bam
error : cannot open reference GTF file - for reading

any help ?

rna-seq • 1.9k views
ADD COMMENTlink modified 3.2 years ago by RamRS27k • written 3.2 years ago by dimitrischat110
1
gravatar for Santosh Anand
3.2 years ago by
Santosh Anand5.1k
Santosh Anand5.1k wrote:

Your command line is wrong. -L specifes labels for different samples, and different samples must be separated by whitespace (not comma; comma seperates the replicates). Also you have not provided any transcripts (GTF/GFF) file.

See manual: http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/

cuffdiff [options]* <transcripts.gtf> \

<sample1_replicate1.sam[,…,sample1_replicateM.sam]> \

<sample2_replicate1.sam[,…,sample2_replicateM.sam]> … \

[sampleN.sam_replicate1.sam[,…,sample2_replicateM.sam]]

transcripts.(gtf/gff)

A transcript annotation file produced by cufflinks, cuffcompare, or other source.

sample1.(sam/bam/cxb)

A SAM file of aligned RNA-Seq reads. If more than two are provided, Cuffdiff tests for differential expression and regulation between all pairs of samples.

ADD COMMENTlink written 3.2 years ago by Santosh Anand5.1k

whitespace is ...\ .. right ?

also if i cant run cufflinks how will i get the trascripts .gtf file? "produced by cufflinks" ..

sorry i guess its a "stupid" question . Thanks for your reply

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by dimitrischat110

whitespaces normally means SPACEs or TABs.

you may like to follow this protocol http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by Santosh Anand5.1k

If this answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

ADD REPLYlink written 3.2 years ago by WouterDeCoster44k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1210 users visited in the last hour