Changes between Version 8 and Version 9 of SOPs/miningSAMBAM


Ignore:
Timestamp:
04/17/14 11:09:02 (11 years ago)
Author:
thiruvil
Comment:

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  • SOPs/miningSAMBAM

    v8 v9  
    8484samtools view -b accepted_hits.bam |samtools fillmd -e - /nfs/genomes/mouse_mm10_dec_11_no_random/fasta_whole_genome/mm10.fa|more
    8585}}}
     86
     87
     88=== Use QualiMap to get (visual) summary of mapping eg. coverage/distribution ===
     89{{{
     90Graphical interface: enter 'qualimap' on the command line
     91
     92Command line:
     93qualimap bamqc -bam myFile.bam -outdir output_qualimap
     94}}}