User: asif.zubair
asif.zubair • 0
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Posts by asif.zubair
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... yes, but since the `vcf` option is being used then the variant IDs should be assigned in the VCF file itself. ...
written 2.6 years ago by
asif.zubair • 0
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... Yes, it turns out there is a problem with flybase's gff file. It seems flybase people fixed that in a newer version.
Thank you for pointing it out!
...
written 4.9 years ago by
asif.zubair • 0
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... Hi,
I got a `gff` file from flybase that i am trying to use with `bedtools`. However, it is throwing an error:
(0)> bedtools intersect -a my.vcf -b dmel-2L-r5.41.gff
Error: Invalid record in file dmel-2L-r5.41.gff. Record is
2L FlyBase chromosome_band -204333 1326937 . ...
written 4.9 years ago by
asif.zubair • 0
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... I am trying to use xdformat to make xdf files from fasta files downloaded from REPBASE - http://www.girinst.org/server/archive/RepBase14.04 .
I concatenated all the references:
cat RepBase14.04.fasta/*.ref RepBase14.04.fasta/appendix/*.ref > repbase_all.fasta
and ran the following command u ...
written 5.0 years ago by
asif.zubair • 0
• updated
2.5 years ago by
Biostar ♦♦ 20
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2.6 years ago,
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For bedtools not working with gff from flybase
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4.9 years ago,
created an answer that has been accepted.
For C: bedtools not working with gff from flybase
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