From dcb8a966d7f029afbfe8a7c292b23a71c4b1741b Mon Sep 17 00:00:00 2001 From: cmargerum Date: Thu, 14 Sep 2017 10:22:51 -0700 Subject: [PATCH] Update Running Platypus Docker --- Platypus/Running Platypus Docker | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/Platypus/Running Platypus Docker b/Platypus/Running Platypus Docker index fdad472..4186026 100644 --- a/Platypus/Running Platypus Docker +++ b/Platypus/Running Platypus Docker @@ -44,7 +44,7 @@ We need to prep your bam file for Opossum and Platypus, do so by entering: samtools index $input samtools view $input -b -o SAMPLE_PREOPOSSUM.bam chrZ:x-y -samtools calmd SAMPLE_PREOPOSSUM.bam /data/ref/$refgenome +samtools calmd –b SAMPLE_PREOPOSSUM.bam /data/ref/$refgenome > SAMPLE_PREOPOSSUM.calmd.bam Note: Replace SAMPLE_PREOPOSSUM.bam with the name you wish for the output and change chrZ:x-y with @@ -57,11 +57,13 @@ Now your file is ready for Opossum. Platypus typically only works on DNA samples through and adds the introns back into the samples, so Platypus doesn't get confused. Run Opossum on your file with the following command: -python /root/Opossum/Opossum.py --SoftClipsExist=True --BamFile=SAMPLE_PREOPOSSUM.bam --OutFile=SAMPLE_POSTOPOSSUM.bam +python /root/Opossum/Opossum.py \ +--SoftClipsExist=True \ +--BamFile=SAMPLE_PREOPOSSUM.calmd.bam \ +--OutFile=SAMPLE_POSTOPOSSUM.bam Note: -Replace SAMPLE_PREOPOSSUM.bam and SAMPLE_POSTOPOSSUM.bam - +Replace SAMPLE_PREOPOSSUM.bam, SAMPLE_POSTOPOSSUM.bam, and SAMPLE_POSTOPOSSUM.calmd.bam 7. Platypus is now able to handle your file. Run it with the following command: