Changes between Version 19 and Version 20 of SOPs/miningSAMBAM

Timestamp:

11/17/14 10:36:55 (10 years ago)

Author:

thiruvil

Comment:

--

SOPs/miningSAMBAM

@@ -113 +113 @@
 unset DISPLAY  #needed for submitting to cluster
 bsub "qualimap bamqc -bam myFile.bam -outdir output_qualimap"
+
 #rnaseq qc
 bsub "qualimap rnaseq -bam myFile.bam -gtf Homo_sapiens.GRCh37.72.canonical.gtf -outdir output_qualimap_rnaseq -protocol non-strand-specific"
+
+#counts qc (after using htseq-count or 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.
+#Sample Condition       Path    Column
+HMLE1   HMLE    totalCounts.txt 2
+HMLE2   HMLE    totalCounts.txt 3
+HMLE3   HMLE    totalCounts.txt 4
+N81     N8      totalCounts.txt 5
+N82     N8      totalCounts.txt 6
+N83     N8      totalCounts.txt 7
+
 }}}
 
@@ -162 +175 @@
 
 }}}
+
+