# HG changeset patch # User nilesh # Date 1373559799 14400 # Node ID 2f55e1d520cd49f61fb29470d60993ea553208a7 # Parent 6f150036a010c6eb5d2f4ab199e636b9511d1584 Uploaded diff -r 6f150036a010 -r 2f55e1d520cd bam_stat.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bam_stat.xml Thu Jul 11 12:23:19 2013 -0400 @@ -0,0 +1,49 @@ + + + reads mapping statistics for a provided BAM or SAM file. + + + rseqc + s + + bam_stat.py -i $input -q $mapqual > $output + + + + + + + + + +.. image:: https://code.google.com/p/rseqc/logo?cct=1336721062 + +----- + +About RSeQC ++++++++++++ + +The RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. “Basic modules” quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while “RNA-seq specific modules” investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation. + +The RSeQC package is licensed under the GNU GPL v3 license. + +Inputs +++++++++++++++ + +Input BAM/SAM file + Alignment file in BAM/SAM format. + +Minimum mapping quality + Minimum mapping quality for an alignment to be called “uniquely mapped” (default=30) + +Output +++++++++++++++ + +- Total Reads (Total records) = {Multiple mapped reads} + {Uniquely mapped} +- Uniquely mapped Reads = {read-1} + {read-2} (if paired end) +- Uniquely mapped Reads = {Reads map to '+'} + {Reads map to '-'} +- Uniquely mapped Reads = {Splice reads} + {Non-splice reads} + + + + \ No newline at end of file