Hi all,
Sorry I'm aware this has been covered but I've tried the various responses already posted and none of which, unfortunately, have worked. I'm struggling to get the cuffdiff commands to work.
I've aligned my sequence file (bacterial RNA-seq genome) using tophat:
tophat -p 8 -G ~/John/ChIP-seq/reference_genome/indexed_genomes/tophat/pSVEN.gff -o ~/John/tophat_rna-seq/psven15/1_psven15 --no-novel-juncs ~/John/ChIP-seq/reference_genome/indexed_genomes/tophat/pSVEN.fa ~/John/RNA-seq/unmodified_seq_files/Sven-WT-8h-minus5PP_S6_R1_001_trimmed.fastq
This appears to have worked fine.
I'm carrying out cuffdiff as described in the protocal, here is my commandline:
cuffdiff -o diff_out6 -b ~/John/ChIP-seq/reference_genome/indexed_genomes/tophat/pSVEN.fa -p 8 -u ~/John/ChIP-seq/reference_genome/indexed_genomes/tophat/pSVEN.gff -L WT,RsrR\
~/John/tophat_rna-seq/psven15/5_psven15/accepted_hits.bam ~/John/tophat_rna-seq/psven15/7_psven15/accepted_hits.bam
I get the error:
You are using Cufflinks v2.2.1, which is the most recent release.
Error: cuffdiff requires at least 2 SAM files
I've tried several iterations of this, minus labels (-L), i orginally had white space character (as is in the paper) behind the "". I've tried with "~/John/..." "./John/..." and "/John/..." for paths.
All paths can be identified with "ls" and .bam files can be converted to .sam files by "samtools view -h".
Any help would be greatly appreciated!
Sorry I'm aware this has been covered but I've tried the various responses already posted and none of which, unfortunately, have worked. I'm struggling to get the cuffdiff commands to work.
I've aligned my sequence file (bacterial RNA-seq genome) using tophat:
tophat -p 8 -G ~/John/ChIP-seq/reference_genome/indexed_genomes/tophat/pSVEN.gff -o ~/John/tophat_rna-seq/psven15/1_psven15 --no-novel-juncs ~/John/ChIP-seq/reference_genome/indexed_genomes/tophat/pSVEN.fa ~/John/RNA-seq/unmodified_seq_files/Sven-WT-8h-minus5PP_S6_R1_001_trimmed.fastq
This appears to have worked fine.
I'm carrying out cuffdiff as described in the protocal, here is my commandline:
cuffdiff -o diff_out6 -b ~/John/ChIP-seq/reference_genome/indexed_genomes/tophat/pSVEN.fa -p 8 -u ~/John/ChIP-seq/reference_genome/indexed_genomes/tophat/pSVEN.gff -L WT,RsrR\
~/John/tophat_rna-seq/psven15/5_psven15/accepted_hits.bam ~/John/tophat_rna-seq/psven15/7_psven15/accepted_hits.bam
I get the error:
You are using Cufflinks v2.2.1, which is the most recent release.
Error: cuffdiff requires at least 2 SAM files
I've tried several iterations of this, minus labels (-L), i orginally had white space character (as is in the paper) behind the "". I've tried with "~/John/..." "./John/..." and "/John/..." for paths.
All paths can be identified with "ls" and .bam files can be converted to .sam files by "samtools view -h".
Any help would be greatly appreciated!
Comment