Problem with annotation file
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#6 Problem with annotation file
I ty to use rna using tophat2 and some data from exome:
I download annot.usc.tx from sourceforge site
[sbsuser@compute-00-01 Integra]$ /illumina/software/PROG2/INTEGRATE_0_2_6/Integrate/bin/Integrate fusion /illumina/software/database/database_2016/hg19_primary.fa /illumina/software/PROG2/annot.ucsc.txt /illumina/software/PROG2/INTEGRATE_0_2_6/Integrate/bwts/ /illumina/runs/FASTQ/Analisiagosto2013b/ALIGN/Sample_R15_sort_rg_order.bam /illumina/runs/FASTQ/Analisiagosto2013b/ALIGN/Sample_R15_sort_rg_order.bam /illumina/runs/FASTQ/Analisi_15novembre2016/Prova3/ALIGN/411/Coclean/411.sorted.dup.recal.cleaned.bam /illumina/runs/FASTQ/Analisi_15novembre2016/Prova3/ALIGN/411/Coclean/412.sorted.dup.recal.cleaned.bam
INTEGRATE version 0.2.6
Loading reference...
chr1 1 249250621
chr2 249250622 492449994
chr3 492449995 690472424
chr4 690472425 881626700
chr5 881626701 1062541960
chr6 1062541961 1233657027
chr7 1233657028 1392795690
chr8 1392795691 1539159712
chr9 1539159713 1680373143
chr10 1680373144 1815907890
chr11 1815907891 1950914406
chr12 1950914407 2084766301
chr13 2084766302 2199936179
chr14 2199936180 2307285719
chr15 2307285720 2409817111
chr16 2409817112 2500171864
chr17 2500171865 2581367074
chr18 2581367075 2659444322
chr19 2659444323 2718573305
chr20 2718573306 2781598825
chr21 2781598826 2829728720
chr22 2829728721 2881033286
chrX 2881033287 3036303846
chrY 3036303847 3095677412
chrM 3095677413 3095693983
4.87 seconds
Loading genes...
error loading genes at: uc001aaa.3 chr1 + 11873 14409 3 11873,12612,13220, 12227,12721,14409, DDX11L1
From 0.3.0, INTEGRATE also use cdsStart and cdsEnd, check your annotation file should have 11 columns.
Could you please help?
I have also another question. I have also STAR alignment can I use?
Hi Mauro,
You can try using the file annot.ensembl.txt at https://sourceforge.net/projects/integrate-fusion/files.
There is also a wiki page about creating gene annotation file for INTEGRATE, https://sourceforge.net/p/integrate-fusion/wiki/annotation/.
Thanks,
Jin