Difference between revisions of "TXGP RNAseq analysis"
From Marcotte Lab
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+ | == Overview == | ||
+ | * We are using [http://bfast.sf.net bfast] and [http://solidsoftwaretools.com/gf/project/mapreads/ mapreads] as main mappers, because they are reasonably fast and have good sensitivity (error-tolerant), with native color-space support. | ||
+ | * We used two strategies for mapping: (1) to JGI draft genome assembly scaffold, and (2) RefSeq MRNA data from XenBase. These would be combined together in the future (when we have enough gene models). | ||
+ | == Database == | ||
+ | See [[TXGP_Xenbase_Data]]. | ||
== Scripts for BFAST == | == Scripts for BFAST == | ||
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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> | ||
+ | |||
+ | == Differential Expression == | ||
== See also == | == See also == | ||
* https://github.com/MarcotteLabGit/HTseq-toolbox/ (GitHub repository for scripts used in TXGP) | * https://github.com/MarcotteLabGit/HTseq-toolbox/ (GitHub repository for scripts used in TXGP) | ||
* http://linusben.net/wiki/index.php/BFAST (Taejoon's personal document for using BFAST) | * http://linusben.net/wiki/index.php/BFAST (Taejoon's personal document for using BFAST) |
Latest revision as of 12:15, 31 August 2011
Contents |
Overview
- We are using bfast and mapreads as main mappers, because they are reasonably fast and have good sensitivity (error-tolerant), with native color-space support.
- We used two strategies for mapping: (1) to JGI draft genome assembly scaffold, and (2) RefSeq MRNA data from XenBase. These would be combined together in the future (when we have enough gene models).
Database
See TXGP_Xenbase_Data.
Scripts for BFAST
- Prepare csfastq files: csfasta + qual --> fastq
$ solid2fastq -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
Differential Expression
See also
- https://github.com/MarcotteLabGit/HTseq-toolbox/ (GitHub repository for scripts used in TXGP)
- http://linusben.net/wiki/index.php/BFAST (Taejoon's personal document for using BFAST)