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1 ---
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2 title: 'HTML report title'
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3 output:
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4 html_document:
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5 number_sections: true
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6 toc: true
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7 theme: cosmo
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8 highlight: tango
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9 ---
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10
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11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
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12 knitr::opts_chunk$set(
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13 echo = opt$echo,
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14 error = TRUE
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15 )
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16 ```
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17
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18
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19 # Code for computational analysis
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20
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21 ```{r 'step 1'}
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22 opt
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23 ```
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24
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25 ```{r 'ste[ 2'}
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26 res = featureCounts(
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27 files = strsplit(opt$input_bam, ',')[[1]],
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28 # annotation
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29 annot.inbuilt=opt$annot_inbuilt,
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30 annot.ext=opt$annot_ext,
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31 isGTFAnnotationFile=opt$isGTFAnnotationFile,
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32 GTF.featureType=opt$gtf_feature_type,
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33 GTF.attrType=opt$gtf_attr_type,
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34 chrAliases=opt$chr_aliases,
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35
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36 # level of summarization
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37 useMetaFeatures=opt$use_meta_features,
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38
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39 # overlap between reads and features
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40 allowMultiOverlap=opt$allow_multi_overlap,
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41 minOverlap=opt$min_overlap,
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42 largestOverlap=opt$largest_overlap,
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43 readExtension5=opt$read_extension_5,
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44 readExtension3=opt$read_extension_3,
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45 read2pos=opt$read_2_pos,
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46
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47 # multi-mapping reads
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48 countMultiMappingReads=opt$count_multi_mapping_reads,
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49 fraction=opt$fraction,
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50
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51 # read filtering
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52 minMQS=opt$min_mqs,
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53 splitOnly=opt$split_only,
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54 nonSplitOnly=opt$non_split_only,
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55 primaryOnly=opt$primary_only,
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56 ignoreDup=opt$ignore_dup,
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57
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58 # strandness
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59 strandSpecific=opt$strand_specific,
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60
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61 # exon-exon junctions
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62 juncCounts=opt$junc_counts,
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63 genome=opt$genome,
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64
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65 # parameters specific to paired end reads
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66 isPairedEnd=opt$is_paired_end,
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67 requireBothEndsMapped=opt$require_both_ends_mapped,
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68 checkFragLength=opt$check_frag_length,
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69 minFragLength=opt$min_frag_length,
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70 maxFragLength=opt$max_frag_length,
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71 countChimericFragments=opt$count_chimeric_fragments,
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72 autosort=opt$auto_sort,
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73
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74 # miscellaneous
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75 nthreads=opt$n_threads,
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76 maxMOp=opt$max_mop,
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77 reportReads=opt$report_reads
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78 )
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79 str(res)
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80 ```
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81
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82
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