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updated readme

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1 parent a7a55bd commit a0ec91447ba68c40d8b99fce11be64b5ecacbddb gturco committed Jul 31, 2012
Showing with 8 additions and 8 deletions.
  1. +8 −8 README.rst
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16 README.rst
@@ -46,12 +46,12 @@ Inputs
prefer the readable Os01g101010 names over the names like m103430.
-Editing Run File
+Runing Pipeline
::::::::::::::::
- + *Once only*: edit quota.sh to correct path for ``quota-alignment``
- + edit quota.sh to the correct `ORGA`, `ORGB`, `QUOTA`
+ + edit run.sh to the correct `ORGA`, `ORGB`, `QUOTA`, `SDGID`, `QDSGID`
+ under the data directory create a new directory titled ORGA_ORGB with their corresponding beds and fasta eg ``mkdir data/rice_v6_sorghum_v1``
+ + activate screen ``screen``
+ activate virtualenv: ``source ../cns_pipeline/bin/activate``
+ run cmd: ``sh run.sh`` #that will call quota.sh (this will take a long time as it's doing a full blast (lastz) and then all of quota align, then cns pipeline).
+ this will create png's for the dotplots. check those to make sure the quota-blocks look correct.
@@ -60,8 +60,8 @@ Editing Run File
Output files
::::::::::::
- + Query and subject CNS position
- + Missing Exons from ORGA ORGB blast
- + CNS blast to RNA file
- + CNS blast to proteins file
- + CNS assigned to nearest Ortholog
+ + CNSlist (contains start,stop,chr,sequences and 5 prime 3 prime information for gene)
+ + Genelist (one for each ORG, contains the gene start,stop,local dupinfo,orthos,number of CNSs)
+ + new genes are named ORG_chr_start_stop in the Genelist
+ + CNS with hits to rna or protein are also renamed in the Genelist
+

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