RNASeq @ BioHPC

RNASeq PIPELINE DESCRIPTION:

The transcriptomics pipeline consists of the following steps:
(1) Parsing the annotation to extract exons, exon-junctions, transcripts and genes
(2) Indexing the genome
(3) Aligning reads against the genome (can be somewhat time-consuming!)
(4) Aligning the reads that do not align to the genome against the exon-junctions
(5) Calculating the coverage of exons, transcripts and genes

The parsing of the annotation and the indexing of the genome have already been run, just choose which genome annotation you are running your sequence against.

OUTPUT:

Gene coverage file contains the following 5 columns:

> gene_name
> name of the highest-rpkm transcript-isoform for the gene
> length of the selected transcript
> rpkm of the selected transcript
> weighted coverage of the selected transcript

References

Nat Genet. 2010 Oct 31.

The developmental dynamics of the maize leaf transcriptome.

Li P, Ponnala L, Gandotra N, Wang L, Si Y, Tausta SL, Kebrom TH, Provart N, Patel R, Myers CR, Reidel EJ, Turgeon R, Liu P, Sun Q, Nelson T, Brutnell TP.
[1] Boyce Thompson Institute, Cornell University, Ithaca, New York, USA. [2] These authors contributed equally to this work.

PMID: 21037569 [PubMed - as supplied by publisher]

Calculations will be carried out on the BioHPC compute cluster at CBSU. You will receive e-mail notifications when the job is submitted, when it starts, and when it is finished. Output will be available via links embedded in the notification e-mails. For more information about this program and BioHPC interface in general, please visit our Frequently Asked Questions page.

Please acknowledge us in all publications and presentation of work that used our resources using the following text.

You must be a registered user of BioHPC to run RNASeq. Please login.

Select genome annotation:
Don't see the genome you need? Contact us!

Select sequence file:

No active registered or pipeline files satisfy the selection criteria

Register output files (.sam files only) for future use within BioHPC
Enter short description of output file to be registered:

Options:

	Prefix for intermediate and output file names.
	Strand specific mapping (both strands will be used)
	number of mismatches allowed (edit distance), for genome alignment
	max number of alignmenrs reported for each read (genome alignment)
	number of mismatches allowed (edit distance), for junction alignment
	max number of alignmenrs reported for each read (junction alignment)

Cluster: This application can't run at this time - no suitable clusters
or you are not authorized to use the service.
The service is available only to Cornell students, faculty, and staff. ( Show timeout info )