Empty output of cufflinks

[gwh120104]

Hi, everyone. I am new in the NGS technology. I need some help about cufflinks.

Currently, I want to get some assembled alignment results of e coli whole genome sequencing data. I downloaded the sra file of e coli whole genome sequencing data from the NCBI SRA website (http://www.ncbi.nlm.nih.gov/sra) and convert it to fastq files via sra toolkit. I installed bowtie2, tophat and cufflinks on a EC2 machine. I tried two pre-built reference genome files from the NCBI and UCSC, respectively(http://support.illumina.com/sequenci...e/igenome.html). I used tophat to do the alignment and I can get the results, 'accepted_hit.bam'. Then I ran the cufflinks. I got empty "transcripts.gtf". Could you help me with these. Thanks a lot!

P.S. Here are the command line I used
SRA convert: fastq-dump SRR1706196.sra
tophat: tophat -p -8 genome SRR1706196.fataq
cufflinks: time cufflinks -p 8 accepted_hit.bam

[GenoMax]

SRR1706196 is a WGS dataset. On other hand tophat/cufflinks are meant for analysis of RNAseq data.

Are you trying to learn analyzing RNAseq data?

[gwh120104]

Actually, I plan to analyse RNAseq data in the future. But currently I want to use the tophat/cufflinks to align and assemble the WGS data. Can I do it? Or are there any other approaches? Thanks!

[GenoMax]

tophat/cufflinks are designed to align expressed sequences to a reference genome. So they would be appropriate to use in future when you are trying to analyze RNAseq data.

If you are looking for alignment programs for NGS data then start with bwa, bowtie/bowtie2, BBMap etc. Assembly programs are more complex but options there would be SPAdes (for bacterial genomes), Velvet, SOAP, ALLPATHS, DiscovarDeNovo etc.

[gwh120104]

Thank you very much! So using tophat/cufflinks is not a good choice for the simple alignment and assembly of WGS data. I will think about it.