# HG changeset patch # User stef # Date 1402671685 14400 # Node ID beb7abe277b3555bbe312c713d1c0a2468dcd9a6 # Parent d4747215fa6b849a8ae37a6f7daeabacee4dabca Uploaded diff -r d4747215fa6b -r beb7abe277b3 QDNAseq.xml --- a/QDNAseq.xml Fri Jun 13 09:53:08 2014 -0400 +++ b/QDNAseq.xml Fri Jun 13 11:01:25 2014 -0400 @@ -1,8 +1,9 @@ - + QDNASEQ_SCRIPT_PATH R + bioc_qdnaseq Quantitative copy number abberation detection @@ -292,24 +293,16 @@ .. class:: warningmark -Requires internet access for downloading bin-annotations from bitbucket and to show css styling of the final report +The input BAMs are expected to be **single end reads of 50bp length** mapped to GRCh37/hg19 genome build. Other experiment setups are currently not supported within galaxy. See the documentation of QDNAseq at bioconductor on how to deal with different setups. .. class:: warningmark -All R stderr is rerouted to stdout due to limitations in R. This means the tool might be marked succesful (green) while it actually isn't, closer inspection of the stdout output is required in that case. - -.. class:: warningmark - -The smaller the binsize, the longer the analysis takes +Requires **internet access** for downloading bin-annotations from bitbucket and to show css styling of the final report .. class:: warningmark If the data is noisy, a **larger binsize** should be chosen -.. class:: warningmark - -The input BAMs are expected to be **single end reads of 50bp length** mapped to GRCh37/hg19 genome build. Other experiment setups are currently not supported within galaxy. See the documentation of QDNAseq at bioconductor on how to deal with different setups. - ----- **Example**