Changes between Version 3 and Version 4 of SOPs/coordinates
- Timestamp:
- 11/04/15 08:24:16 (9 years ago)
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SOPs/coordinates
v3 v4 62 62 }}} 63 63 64 === convert bam to bigwig ===64 === Convert bam to bigwig === 65 65 {{{ 66 66 Step1: convert bam to bedGraph format: … … 73 73 }}} 74 74 75 === Updat ing/fixingUCSC GTF file ===75 === Update/fix UCSC GTF file === 76 76 77 77 * GTF files from UCSC Table Browser use RefSeq (NM* ids) for both gene_id and transcript_id which may not be compatible for some programs (eg. counting by genes using HTSeq) … … 104 104 Ex: bed2gff.pl foo.bed WIBR exon > foo.gff 105 105 }}} 106 107 === Split bed file by chromosome === 108 109 * Sometimes it's easier working with only one chromosome of regions at a time 110 * Output files will be named like "Sample_1.chr1.bed". 111 112 {{{ 113 awk '{close(f);f=$1}{print > "Sample_1."f".bed"}' Sample_1_all_chrs.bed 114 }}} 106 115 107 116 === Convert gtf to bed === … … 163 172 164 173 165 === create wiggle files for visualizing paired-end data mapping to the + and - strands ===174 === Create wiggle files for visualizing paired-end data mapping to the + and - strands === 166 175 167 176 1. split by strand by matched strand
