Changes between Version 26 and Version 27 of SOPs/SAMBAMqc

Timestamp:

08/20/20 10:58:04 (5 years ago)

Author:

gbell

Comment:

--

SOPs/SAMBAMqc

@@ -72 +72 @@
 
 ==== [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
-# Command line:
+
+{{{
+# For Graphical interface (with GUI access to all tools)
+qualimap
+
+# Full command on the command line:
 unset DISPLAY  #needed for submitting to cluster
 bsub "qualimap bamqc -bam myFile.bam -outdir output_qualimap"
 # For huge data, you can increase memory with --java-mem-size="4800M" to avoid OutOfMemoryError: Java heap space
 
-
-#rnaseq qc
+# For rnaseq QC
 bsub "qualimap rnaseq -bam myFile.bam -gtf Homo_sapiens.GRCh37.72.canonical.gtf -outdir output_qualimap_rnaseq -p non-strand-specific"
 
-#counts qc (after using htseq-count or similar program to generate a matrix of counts)
+# For counts QC (after using htseq-count or a similar program to generate a matrix of counts)
 qualimap counts -d countsqc_input.txt -c -s HUMAN -outdir counts_qc
 #Format of countsqc_input.txt (below), totalCounts.txt is a matrix of counts; header lines must be commented "#" and species is human or mouse only.
@@ -93 +95 @@
 N82     N8      totalCounts.txt 6
 N83     N8      totalCounts.txt 7
-
 }}}