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arq5x / bedtools2

bedtools - the swiss army knife for genome arithmetic
MIT License
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refGene.txt hq19 - file turncated #842

Open joni73 opened 4 years ago

joni73 commented 4 years ago

joni@mpi1:~/ASIAT/DNA$ bedToBam -i /home/joni/ASIAT/DNA/56001801066357A.snp.vcf -g /mpi3/S5/annovar/humandb/refGene.txt > kani1snp.bam joni@mpi1:~/ASIAT/DNA$ samtools view kani1snp.bam [main_samview] truncated file. joni@mpi1:~/ASIAT/DNA$

It work's hq18 database but not hq19 downloaded http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/refGene.txt.gz

as I understand it's .bed format ?

joni73 commented 4 years ago

Have tried whit difrently formed file,....

wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz joni@mpi1:~/ASIAT/DNA$ bedtools sort -i /mpi3/S5/annovar/humandb/knownGene.txt > /mpi3/S5/annovar/humandb/knownGene.sorted.txt Error: malformed GFF entry at line 79482. Start was greater than end. Exiting. joni@mpi1:~/ASIAT/DNA$

joni73 commented 4 years ago

Ubuntu 18.04 Version: v2.26.0

joni73 commented 4 years ago

Version: v2.29.2-25-g3dd63c46 joni@mpi1:~/ASIAT/DNA$ /mpi3/S5/bedtools2/bin/bedtools sort -i /mpi3/S5/annovar/humandb/knownGene.txt > /mpi3/S5/annovar/humandb/knownGene.sorted.txt Error: malformed GFF entry at line 79482. Coordinate detected that is < 1. Exiting.

arq5x commented 4 years ago

I am confused about what your problem is. What file?

maximilianh commented 1 year ago

refGene.txt is not in BED format. But you can convert it to BED: https://github.com/ken0-1n/refgenetxttobed