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Elementolab/small RNA-seq pipeline

Ole2001 — Sat, 11 May 2013 17:57:27 GMT

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

Tas2019 — Fri, 10 May 2013 01:47:25 GMT

/* 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===

Ole2001 — Thu, 09 May 2013 23:57:11 GMT

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
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	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

Kwe2001 — Mon, 22 Apr 2013 19:15:47 GMT

Revision as of 19:15, 22 April 2013		Current revision
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	scp -r -i ~/.ssh/yourawskey.pem pmpca/ ec2-user@ec2-50-19-32-49.compute-1.amazonaws.com:/home/ec2-user/portal-data/studies/		scp -r -i ~/.ssh/yourawskey.pem pmpca/ ec2-user@ec2-50-19-32-49.compute-1.amazonaws.com:/home/ec2-user/portal-data/studies/
		+

	Login and load data		Login and load data

Tas2019 — Thu, 18 Apr 2013 16:27:57 GMT

/* Print the content of a binary wiggle file */

Revision as of 16:27, 18 April 2013		Current revision
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	-o Output binary Wiggle file		-o Output binary Wiggle file
	-res Resolution (bin size)		-res Resolution (bin size)
		+	--norm Normalize by resolution (i.e. calculate average read count instead of total read count)
		+	--peak Treat each record as a peak (i.e. ignore column 4 and add count 1)

	===Print the content of a binary wiggle file===		===Print the content of a binary wiggle file===
	./geneModel chip -cmd print-bin-wig [options]		./geneModel chip -cmd print-bin-wig [options]
	-i Binary wiggle file		-i Binary wiggle file
		+	--interval Print in ChIP-seq interval format (by default is off, i.e. shows in the internal format)
		+	--avg Show average read count instead of total read count (i.e. normalize by bin size)
		+	--smooth
		+	-k
		+	--nonzero If specified, print only the non-zero entries

	===Extend the peak intervals by n-bp on each side===		===Extend the peak intervals by n-bp on each side===

Tas2019 — Thu, 18 Apr 2013 15:35:46 GMT

Revision as of 15:35, 18 April 2013		Current revision
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	* Which genomes does geneTools support?		* Which genomes does geneTools support?
	Ans:		Ans:
-	Currently we only support the human genome (hg18 and hg19) but are working on incorporating additional ones. Please let us know if there are genomes you'd like us to support.	+	Currently we only support the human genome (hg18 and hg19) but are working on incorporating additional ones. An experimental version supports mouse (mm9, mm10), drosophila (dm3), and C. elegans (ce6, ce10). Please let us know if there are genomes you'd like us to support.

	== Related pages ==		== Related pages ==
	* [[GeneTools]]		* [[GeneTools]]
	* [[GeneTools installation]]		* [[GeneTools installation]]