Hello readers,
I've been working on a computational pipeline to analyze RNA-Seq data in order to detect alternatice splicing and chimeric transcripts. It got published last month in Nucleic Acid Research. Please find the paper at:
http://nar.oxfordjournals.org/content/early/2012/01/28/nar.gks047.long
The program is freely available at: www.mcdonaldlab.biology.gatech.edu/r-sap.htm.
The pipeline is actively under development so feel free to use it and any suggestions and feedbacks are most welcome.
Hi Vinay,
ReplyDeleteI am new to bioinformatic field. your blog help me a lot in analysis NGS data's. At present i started working on RNA-SEQ. I have come across about R-SAP through your blog. I am working on arabidopsis rna-seq data. Can you guide me how to convert the fastq file to Psl/Pslx file
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ReplyDeleteHi Saranya,
ReplyDeleteThanks for your interest. This pipeline works well and accurately for assembled contigs from the short-read data or longer reads (such as from 454 or PacBio sequencing technologies).
Since you have FastQ files, I presumably you will have short-read sequence data. I suggest you to do the assembly first (reference based using Cufflinks or Scripture if you are interested in detecting novel splice variants ) or de-novo assembly using Trans-ABySS or trinity (or any other similar program) if you are interested in detecting fusion-gene transcripts.
For reference-based assembly, you can directly supply resulting GTF or BED files to R-SAP but for de-novo assembly, you will have to align the assembled contigs to the reference genome using SSAHA2 or BLAT. Then you can use resulting psl/pslx files with R-SAP.
If you are inclined to use your short-read sequence data directly with R-SAP then try aligning them to the reference genome using SSAHA2 and then run R-SAP on the alignment file. But this way you will get a lot of noise in the final output.
Hope this helps.
Thank you vinay
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