Changes between Initial Version and Version 1 of BIOS_ReferenceFiles/MetaExonAnnotation_documentation

Timestamp:

Sep 19, 2016 4:48:45 PM (8 years ago)

Author:

jamverlouw

Comment:

--

BIOS_ReferenceFiles/MetaExonAnnotation_documentation

@@ +1 @@
+= Meta-exon annotation =
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+
+To create the meta-exon annotation the following steps were taken: [[BR]]
+1. The exon annotation from Ensembl Biomart v.71 was downloaded. The file contained the following columns: [[BR]]chromosome, exon start, exon end, Ensembl exon id, Ensembl gene id, gene name, strand.[[BR]]
+2. All additional contigs (GL*, LRG* etc) were removed, so that only ordinary chromosomes (1-22, X, Y, MT) remained. This was done by a custom script cutStrangeChr.py (see attachment). [[BR]]
+3. The Biomart file was converted to bed format and sorted by start coordinate:[[BR]]
+4. Exons were merged using mergeBed tools from BEDTools suite:[[BR]]
+5. The resulting file was converted to gtf format, retaining the strand information by a custom script mergedBed_to_gtf.py (see attachment).[[BR]]
+
+
+The final commands to generate the meta-exon annotation were the following:[[BR]][[BR]]
+{{{./cutStrangeChr.py biomart_export.txt | awk 'BEGIN {FS="\t"}; {OFS="\t"}; {if ($7 == "-1") $7 = "-"; else $7 = "+"}; {print $1, $2 - 1, $3, $4 ":" $5 ":" $6, ".", $7}' | sort -k1,1n -k2,2n | mergeBed -nms -d -1 -i stdin > biomart_export.merged.tmp}}}[[BR]][[BR]]
+{{{./mergedBed_to_gtf.py biomart_export.merged.tmp biomart_export.txt | sort -k1,1n -k4,4n > meta-exons_v71_cut_sorted_18-04-14.gtf}}}
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