Difference between revisions of "TXGP RNAseq analysis"

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(Scripts)
(Scripts)
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== Scripts ==
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== Scripts for BFAST ==
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* Prepare csfastq files: csfasta + qual --> fastq
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$ solid2fastq -n 10000000 -o reads foobar.csfasta foobar_QV.qual
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* Prepare database sequences. Multiple indexes are not used yet.
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<pre>$ bfast fasta2brg -f mygenome.fa -A 1
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$ bfast fasta2brg -f mygenome.fa
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$ bfast index -f mygenome.fa -m 1111111111111111111111 -d 1 -w 14 -A 1</pre>
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* run-bfast-match.sh : a script to map csfastq reads to FASTA file.
 
* run-bfast-match.sh : a script to map csfastq reads to FASTA file.
 
<pre>#!/bin/bash
 
<pre>#!/bin/bash
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   echo "Usage: run-bfast-match.sh <DB fasta file>"
 
   echo "Usage: run-bfast-match.sh <DB fasta file>"
 
fi</pre>
 
fi</pre>
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 +
== See also ==
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* https://github.com/MarcotteLabGit/HTseq-toolbox/ (GitHub repository for scripts used in TXGP)
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* http://linusben.net/wiki/index.php/BFAST (Taejoon's personal document for using BFAST)

Revision as of 14:23, 14 June 2011


Scripts for BFAST

  • Prepare csfastq files: csfasta + qual --> fastq
$ solid2fastq -n 10000000 -o reads foobar.csfasta foobar_QV.qual
  • Prepare database sequences. Multiple indexes are not used yet.
$ bfast fasta2brg -f mygenome.fa -A 1
$ bfast fasta2brg -f mygenome.fa
$ bfast index -f mygenome.fa -m 1111111111111111111111 -d 1 -w 14 -A 1
  • run-bfast-match.sh : a script to map csfastq reads to FASTA file.
#!/bin/bash
FASTA=$1
if [[ -f $FASTA ]];
then
  echo "File:",$FASTA
  for FASTQ in $(ls ../fastq/*.fastq.gz)
  do
    BASENAME=$(basename $FASTQ)
    BMF=${BASENAME/".fastq.gz"/}".bmf"
    BAF=${BASENAME/".fastq.gz"/}".baf"
    SAM=${BASENAME/".fastq.gz"/}".sam"
    echo "$FASTQ -- $FASTA --> $SAM"
    bfast match -A 1 -n 4 -f $FASTA -r $FASTQ -z > $BMF
    bfast localalign -A 1 -n 4 -f $FASTA -m $BMF > $BAF
    bfast postprocess -A 1 -n 4 -f $FASTA -i $BAF > $SAM
  done
else
  echo "Usage: run-bfast-match.sh <DB fasta file>"
fi

See also