Changes between Version 17 and Version 18 of SOPs/miningSAMBAM


Ignore:
Timestamp:
06/04/14 14:38:27 (11 years ago)
Author:
thiruvil
Comment:

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  • SOPs/miningSAMBAM

    v17 v18  
    9797=== QC to get a (visual) summary of mapping statistics.  For eg. coverage/distribution of mapped reads across the genome or transcriptome. ===
    9898
    99 ==== RSeQC: RNA-Seq quality control package ====
     99==== RSeQC: RNA-Seq quality control package for getting mapping statistics (eg. unique/multi-mapped reads) ====
    100100{{{
    101 #get mapping statistics (eg. unique/multi-mapped reads)
    102101bam_stat.py -i myFile.bam
    103102}}}
    104103
    105 ==== QualiMap: can be used on DNA or RNA-Seq ====
     104==== Picard: CollectRnaSeqMetrics.jar to find coverage across gene body for 5' or 3' bias ====
     105{{{
     106java -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
     107}}}
     108
     109==== QualiMap: can be used on DNA or RNA-Seq to get summary of mapping and coverage/distribution ====
    106110{{{
    107111# Graphical interface: enter 'qualimap' on the command line