Changes between Version 20 and Version 21 of SOPs/miningSAMBAM

Timestamp:

11/17/14 10:43:37 (10 years ago)

Author:

thiruvil

Comment:

--

SOPs/miningSAMBAM

@@ -97 +97 @@
 === QC to get a (visual) summary of mapping statistics.  For eg. coverage/distribution of mapped reads across the genome or transcriptome. ===
 
-==== RSeQC: RNA-Seq quality control package for getting mapping statistics (eg. unique/multi-mapped reads) ====
+==== [http://rseqc.sourceforge.net/ | RSeQC]: RNA-Seq quality control package for getting mapping statistics (eg. unique/multi-mapped reads) ====
 {{{
 bam_stat.py -i myFile.bam
 }}}
 
-==== Picard: CollectRnaSeqMetrics.jar to find coverage across gene body for 5' or 3' bias ====
+==== [http://broadinstitute.github.io/picard/ | Picard]: CollectRnaSeqMetrics.jar to find coverage across gene body for 5' or 3' bias ====
 {{{
 java -jar /usr/local/share/picard-tools/CollectRnaSeqMetrics.jar INPUT=accepted_hits.bam REF_FLAT=refFlat.txt STRAND_SPECIFICITY=NONE OUTPUT=Out_RnaSeqMetrics.txt REFERENCE_SEQUENCE=hg19.fa CHART_OUTPUT=Out_RnaSeqMetrics.pdf
 }}}
 
-==== QualiMap: can be used on DNA or RNA-Seq to get summary of mapping and coverage/distribution ====
+==== [http://qualimap.bioinfo.cipf.es/ | QualiMap]: can be used on DNA or RNA-Seq to get summary of mapping and coverage/distribution ====
 {{{
 # Graphical interface: enter 'qualimap' on the command line