Description Usage Arguments Details Note
View source: R/RNASeqPipelineR.R
Uses Tophat to align reads in FASTQ files against the reference genome hg38 from UCSC database. Optionally you can specify paired end reads. The code assumes paired reads have fastq files that differ by one character (i.e. sampleA_read1.fastq, sampleA_read2.fastq) and will perform matching of paired fastq files based on that assumption using string edit distance. Read 1 is assumed to be upstream and read 2 is assumed to be downstream.
1 2 3 4 5 | sequenceAlignmentTopHat(path = "/shared/silo_researcher/Gottardo_R/jingyuan_working/iGenome/Mus_musculus/UCSC/mm10",
parallel_threads = 1, tophat_threads = 6, paired = FALSE,
nchunks = 10, days_requested = 5, slurm = FALSE,
slurm_partition = "gottardo_r", ram_per_node = tophat_threads *
parallel_threads * 1200)
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path |
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parallel_threads |
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tophat_threads |
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paired |
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nchunks |
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days_requested |
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slurm |
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slurm_partition |
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ram_per_node |
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The number of parallel_threads*tophat_threads should not be more than the number of cores available on your system.
The amount of memory requested should be set to bowtie_threads*parallel_threads*1G as this is the default requested by samtools for sorting. If insufficient memory is requested, the bam files will not be created successfully.
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