Hello All,
Because my data include paired-end reads and single-end reads, so i run the tophat twice as manual recommened. Aslo, two bam files result from only one sample, were produced by Tophat.
I use picard tools to sort two bam files and merge into one sorted_merged.bam file. Then , Cuffdiff was used to perform downstream DE genes analysis. error message appears like this,
File ./combined_thout/sorted_merged.sam doesn't appear to be a valid BAM file, trying SAM...
Error: sort order of reads in BAMs must be the same
The sorted bam files produced by picard were incompatible with other bam files provided by tophat.
Has anyone deal with this condition? Less information about data from different library type were mentioned in cufflink protocol.
Thanks.
Because my data include paired-end reads and single-end reads, so i run the tophat twice as manual recommened. Aslo, two bam files result from only one sample, were produced by Tophat.
I use picard tools to sort two bam files and merge into one sorted_merged.bam file. Then , Cuffdiff was used to perform downstream DE genes analysis. error message appears like this,
File ./combined_thout/sorted_merged.sam doesn't appear to be a valid BAM file, trying SAM...
Error: sort order of reads in BAMs must be the same
The sorted bam files produced by picard were incompatible with other bam files provided by tophat.
Has anyone deal with this condition? Less information about data from different library type were mentioned in cufflink protocol.
Thanks.
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