I'm following the Tuxedo protocol with 100cycle single directional illumina hi Seq 2000 data. I have used Tophat and Bowtie to align my reads to the Arabidopsis genome, I then used Cufflinks to search for splice-variants and Cuffmerge to join the files together. I now want to use Cuffdiff to examine the differential gene and isoform expression but get the following error message...
File ./home/richard/RNA_seq_analysis/run296_tophat/9-0GS_AGTCAA_run296_tophat/accepted_hits.bam doesn't appear to be a valid BAM file, trying SAM... Error: cannot open alignment file
This implies that it can't open the alignment files but i don't know why? When i examined the BAM files that were produced by TopHat, i noticed their icons look like they have been zipped (right click, properties also supports this theory), however i can't unzip them with gunzip (using command line nor GUI methods).
Any ideas?
File ./home/richard/RNA_seq_analysis/run296_tophat/9-0GS_AGTCAA_run296_tophat/accepted_hits.bam doesn't appear to be a valid BAM file, trying SAM... Error: cannot open alignment file
This implies that it can't open the alignment files but i don't know why? When i examined the BAM files that were produced by TopHat, i noticed their icons look like they have been zipped (right click, properties also supports this theory), however i can't unzip them with gunzip (using command line nor GUI methods).
Any ideas?
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