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Elementolab/small RNA-seq pipeline

2013-05-11T17:57:27Z

Revision as of 17:57, 11 May 2013		Current revision
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	* remove adapters		* remove adapters

-	If the adapters have been masked:	+	If the adapters have been masked, eg by the core:

	for f in s_*.txt.gz; do gr_5n "perl /home/ole2001/PROGRAMS/SNPseeqer/SCRIPTS/fastq_remove_N_adapters.pl $f" --name=rem$f; done		for f in s_*.txt.gz; do gr_5n "perl /home/ole2001/PROGRAMS/SNPseeqer/SCRIPTS/fastq_remove_N_adapters.pl $f" --name=rem$f; done
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	Otherwise use Smith-Waterman:		Otherwise use Smith-Waterman:

-	for f in *.gz; do echo $f; gr_5n "/home/ole2001/PROGRAMS/SMITH-WATER/remove_miRNA_adapter $f \| gzip > $f.noadapt.gz" -name S$f ; done	+	for f in *.gz; do echo $f; gr_5n "/home/ole2001/PROGRAMS/SMITH-WATER/remove_miRNA_adapter -fastqfile $f \| gzip > $f.noadapt.gz" -name S$f ; done


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	perl /home/ole2001/PROGRAMS/miRSeeqer/run_miRSeeqer.pl --samples=samples_info.txt --mir=1 --genome=hg19		perl /home/ole2001/PROGRAMS/miRSeeqer/run_miRSeeqer.pl --samples=samples_info.txt --mir=1 --genome=hg19
		+
		+
		+	* run stats analysis
		+
		+	perl ~/PROGRAMS/miRSeeqer/run_miRSeeqer_summarize_stats.pl --samples=sample_infos.txt

2013-05-10T01:47:25Z

/* Generate random mappable regions */

Revision as of 01:47, 10 May 2013		Current revision
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	--norm Mappability track contains normalized scores		--norm Mappability track contains normalized scores
	--block Output randomly selected regions as <res> bp blocks		--block Output randomly selected regions as <res> bp blocks
		+
		+	E.g. This command generates 500 10kb regions with mappability > 0.9. The mappability file is in bed format and contains the mappability score for all 10kb windows in the genome.
		+	./geneModel util -cmd gen-map -i data/mappability_50bp_chr_10K.txt -res 10000 -n 500 --norm -min 0.9

	===Perform Fisher's exact tests===		===Perform Fisher's exact tests===

2013-05-09T23:57:11Z

Revision as of 23:57, 9 May 2013		Current revision
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	* clean up raw files		* clean up raw files

-	perl ~/PROGRAMS/SNPseeqer/SCRIPTS/cassava1.8_merge_move_data.pl --dir="Sa*" --tgtdir=. --exec=1 --pe=0	+	perl ~/PROGRAMS/SNPseeqer/SCRIPTS/casava1.8_merge_move_data_old.pl --dir="Sa*" --tgtdir=. --exec=1 --pe=0

	* remove adapters		* remove adapters
Line 17:		Line 17:

	for f in *.noadapt.gz; do PBS_quickAlign.pl --fastq=$f --bwaidx=/pbtech_mounts/oelab_scratch002/ole2001/DATA/GENOMES/hg19/hg19bwaidx --submit=1; done		for f in *.noadapt.gz; do PBS_quickAlign.pl --fastq=$f --bwaidx=/pbtech_mounts/oelab_scratch002/ole2001/DATA/GENOMES/hg19/hg19bwaidx --submit=1; done
		+
		+	Same for mouse
		+
		+	for f in *.noadapt.gz; do PBS_quickAlign.pl --fastq=$f --bwaidx=/home/ole2001/PROGRAMS/SNPseeqer/REFDATA/mm9/mm9idx --submit=1; done
		+

	* get a sample list		* get a sample list
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	. 5 CA16S CCAACA human		. 5 CA16S CCAACA human
	. 6 CA1S AGTCAA human		. 6 CA1S AGTCAA human
		+
		+
		+	* run miRseeqer
		+
		+	perl /home/ole2001/PROGRAMS/miRSeeqer/run_miRSeeqer.pl --samples=samples_info.txt --mir=1 --genome=hg19
		+

	* add sample group information, eg in a new file called sample_infos.txt.withgroups		* add sample group information, eg in a new file called sample_infos.txt.withgroups