Difference between revisions of "9.2 Read mapping using bwa"

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(Created page with "Read mapping with '''bwa''' is peculiar in which it requires two steps: in the first, bwa produces the mapping using an internal format (called sai fo...")
 
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Read  mapping  with  '''bwa'''  is  peculiar  in  which  it  requires  two  steps:  in  the  first,  bwa  produces  the  mapping  using  an  internal  format  (called  sai  format)  that  is  different  from  the '''BAM/SAM'''  that  you  saw  before.  The  sai  files  need  then  to  be  converted  in  SAM.  Moreover, in case of paired end reads, you will need to process them separately then join  the outputs. You will do both steps in one script. Let’s open a text file called, for example,  bwamapping.sh, in which you can write the usual stuff:  
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Read  mapping  with  '''bwa'''  is  peculiar  in  which  it  requires  two  steps:  in  the  first,  '''bwa''' produces  the  mapping  using  an  internal  format  (called  '''sai''' format)  that  is  different  from  the '''BAM/SAM'''  that  you  saw  before.  The  '''sai''' files  need  then  to  be  converted  in  '''SAM'''.  Moreover, in case of paired end reads, you will need to process them separately then join  the outputs. You will do both steps in one script. Let’s open a text file called, for example,  '''bwamapping.sh''', in which you can write the usual stuff:  
 
   
 
   
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#/bin/bash
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#$ -S /bin/sh
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#PBS -l walltime=4:00:00
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#$ -cwd
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#PBS -l select=1:ncpus=4:mpiprocs=1:mem=16GB
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#$ -q amd.q,large.q,intel.q
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#PBS -A <your account>
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#$ -l h_vmem=16G
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#PBS -W group_list="<your account>"
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#$ -e bwa_mapping.e
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module load profile/bio
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#$ -N bwa_mapping
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module load profile/advanced
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#$ -o bwa_mapping.o
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module load bwa
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module load bwa/0.7.12

Revision as of 16:03, 20 February 2016

Read mapping with bwa is peculiar in which it requires two steps: in the first, bwa produces the mapping using an internal format (called sai format) that is different from the BAM/SAM that you saw before. The sai files need then to be converted in SAM. Moreover, in case of paired end reads, you will need to process them separately then join the outputs. You will do both steps in one script. Let’s open a text file called, for example, bwamapping.sh, in which you can write the usual stuff: 

#$ -S /bin/sh
#$ -cwd
#$ -q amd.q,large.q,intel.q
#$ -l h_vmem=16G
#$ -e bwa_mapping.e
#$ -N bwa_mapping
#$ -o bwa_mapping.o
module load bwa/0.7.12
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