clark-lab Bisulfite_tools issues

clark-lab / Bisulfite_tools

Pipeline for alignment of Illumina bisulfite sequencing data and associated tools

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issues

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CpG_preparation.R to check whether genome is hosted on UCSC before trying to pull down CpG islands

#31 astatham opened 10 years ago
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Add option for NOMe

#30 astatham opened 10 years ago
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Add lambda genome for % conversion

#29 astatham opened 10 years ago
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bedGraph_to_Rdata still uses hg19

#28 astatham opened 10 years ago
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Align to arbitrary genomes

#27 astatham closed 11 years ago
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Add (optional?) FLASh integration

#26 astatham opened 11 years ago
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Pipeline fails if the directory name starts with a number at the first qsub

#25 astatham opened 11 years ago
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Add option to trim sequenom adaptors (needed for MiSeq)

#24 astatham opened 11 years ago
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Integrate MiSeq amplicon alignment

#23 astatham opened 11 years ago
1
add scipen to R scripts that output text

#22 astatham closed 11 years ago
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Split fastqc section into separate qsub

#21 astatham opened 11 years ago
1
Merge PE and SE scripts

#20 astatham opened 11 years ago
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Remove wolfpack specific gunk

#19 astatham opened 11 years ago
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Add fastq_screen to prep_reads

#18 astatham opened 11 years ago
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Run bismark_methylation_extractor on name sorted bam file

#17 astatham closed 11 years ago
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Execute all qsub scripts from the output/ directory

#16 astatham opened 11 years ago
1
Use kevins java to avoid random pipeline failures

#15 astatham closed 11 years ago
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Convert main script over to a Makefile - for free checkpointing

#14 astatham opened 11 years ago
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Keep unaligned and multimapping reads

#13 astatham closed 11 years ago
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Allow single end reads to be processed

#12 astatham closed 11 years ago
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Add number of initial and trimmed reads to alignment_stats

#11 astatham closed 11 years ago
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Create report at end of run

#10 astatham opened 11 years ago
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Always qsub to all.q

#9 astatham closed 11 years ago
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Use pid in qsub job names to avoid clashes

#8 astatham closed 11 years ago
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Improve logs

#7 astatham opened 11 years ago
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Allow any number of chunks (currently hardcoded at 20)

#6 astatham opened 11 years ago
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Update to bismark version 0.8.0

#5 astatham closed 11 years ago
1
Remove trimmed_split directory immediately after merging bam chunks

#4 astatham closed 11 years ago
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Delete chunk fastqs immediately after alignment

#3 astatham closed 11 years ago
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Convert chunk alignment to an array qsub

#2 astatham closed 11 years ago
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Output bams do not have read group tags

#1 astatham closed 11 years ago
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