Dear All

I need some (lots) suggestions and help,  first and most important is that i am 
working on bacterial RNA seq (illumina reads)
my analysis steps are as following ....

Step 1.  FASTQ sequence data was groomed

Step 2. I did mapping by Bowtie with default parameters. Reference genome fasta 
file i am using from my history, because the reference genome is not vaialble 
on galaxy.

Step3. i sorted the bowtie output file using r workflow (Germy Goecks 
workflow)  , link below

Step4. this sorting provided me Concatenate files

Step5. Concatenated files were used to run CUFFLINK, this provided me assembled 
trancript file

Step6: Assembled transcript files from step 5 were used for CUFFMERGE

Step 7:  For CUFFDIFF Transcript GTF file generated from  Step 6and  
concatenate files from step 4 were used 

Now my question is if this workflow is acceptable for bacterial transcriptome 

Should i filter SAM file, if yes then at which step

Should i convert SAM file to the BAM file, then at which step it should be

Is that Ok to use fasta of reference genome for mapping should it be converted 
to any other format, if yes then what should be the workflow

If any one have experince of bowtie parametes to map bacterial RNA seqquence 
analsis are very much welcomed  

Thanking you all 
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