need help--bacterial RNA-seq

[wall_y]

i am a new one on this project, we are doing a bacterial transcriptome using Solid single-end no strand specific sequencing to see transcription difference between two growth conditions.

this bacteria does not have published genome, but we have 454 and solexa sequencing result but not complete, and also have a similar bacterial (many known genes have very high similarity) genome.

i need help on how to use tophat and cufflinks to analysis the data () using the unfinished sequencing or the similar bacterial genome as reference.

many thanks.

[colindaven]

Perhaps a different approach:

Start with the related genome.
Map reads with bioscope, Bowtie etc
Use Bedtools and annotation to count reads mapping to genes.
Put read counts into either R, or a spreadsheet and do some normalisation eg RPKM and testing.
Compare two conditions with Fishers Exact test etc.

[wall_y]

many thanks, i would try this.

Perhaps a different approach:

Start with the related genome.
Map reads with bioscope, Bowtie etc
Use Bedtools and annotation to count reads mapping to genes.
Put read counts into either R, or a spreadsheet and do some normalisation eg RPKM and testing.
Compare two conditions with Fishers Exact test etc.

[qqtwee]

Perhaps a different approach:

Start with the related genome.
Map reads with bioscope, Bowtie etc
Use Bedtools and annotation to count reads mapping to genes.
Put read counts into either R, or a spreadsheet and do some normalisation eg RPKM and testing.
Compare two conditions with Fishers Exact test etc.

Hello, I am analying bacterial transcriptome using solexa paired-end strand specific (SOLiD adapter library) sequencing data, I have no idea how to deal with it. Could you give me some advice on data processing pipeline ,and which tool can I use to deal with strand specific RNA-seq? I am looking forward to your reply, thank you very much! Best wishes!

[swbarnes2]

Hello, I am analying bacterial transcriptome using solexa paired-end strand specific (SOLiD adapter library) sequencing data, I have no idea how to deal with it. Could you give me some advice on data processing pipeline ,and which tool can I use to deal with strand specific RNA-seq? I am looking forward to your reply, thank you very much! Best wishes!

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