Dear All
I am analyzing bacterial transcriptome (illumina paired end reads) via online galaxy server.
After mapping by bowtie and sorting my SAM file, i am using cufflink to get assembled transcript and cuffdiff to find singinicantly different changes,
Quey 1: Could you please suggest, if i could use cufflink for bacterial transcriptome, if yes which paratmetrs i should change in galaxy online version
Query 2: Locus that is shown to be significantly differently expressed is of about 2.5 kb, and it may have more than one gene. would it be possible to see genes annotation or to see significant gene changes. It might be within this locus one gene is upregulated while other is downregulated.
I am analyzing bacterial transcriptome (illumina paired end reads) via online galaxy server.
After mapping by bowtie and sorting my SAM file, i am using cufflink to get assembled transcript and cuffdiff to find singinicantly different changes,
Quey 1: Could you please suggest, if i could use cufflink for bacterial transcriptome, if yes which paratmetrs i should change in galaxy online version
Query 2: Locus that is shown to be significantly differently expressed is of about 2.5 kb, and it may have more than one gene. would it be possible to see genes annotation or to see significant gene changes. It might be within this locus one gene is upregulated while other is downregulated.