I'm very new in BioInformatics (VERY) - please someone help with this:
first I run this command:
bgzip mydata.gff3
Then this is created:
data.gff3.gz
Then I run:
tabix -p gff data.gff3.gz
ths is the error I get
[get_intv] the following line cannot be parsed and skipped:
[ti_index_core] the indexes overlap or are out of bounds
I know there is nothing wrong with my data (it is used in my application elsewhere)
Can someone point me in the right direction to solve this?
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kevin.mohamed1992 •
check that your GFF file is:
thanks, but now there is one error: [ti_index_core] the file out of order at line 19
this is line 19 : ctgA example SNP 1000 1000 0.987 . . ID=FakeSNP1;Name=FakeSNP;Note=This is a fake SNP that should appear at 1000 with length 1
your file is not sorted.
alright - thanks, any direction you can give me with sorting?
There's a note in the tabix documentation for sorting a gff (reproduced below, but I needed to separate the bgzip step separately)
(grep ^"#" in.gff3; grep -v ^"#" in.gff3 | sort -k1,1 -k4,4n) > out.sorted.gff3
bgzip out.sorted.gff3
Another command I found useful to sort gff using awk
awk '$1 ~ /^#/ {print $0;next} {print $0 | "sort -t\"\t\" -k1,1 -k4,4n -k5,5n"}' file.gff > file.sorted.gff
This is similar to the method from http://www.htslib.org/doc/tabix.html but it properly sets the tab delimiter on the sort command and avoids subshells
avoids subshells
well, there is a system call....
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Hey guys!
Sorry about the simplicity of the question! But I'm trying for ours to open a gff in artemis to check some gene models and I can not!! The fasta and sorted bam file work well, but I can not get the gff together at all!!
So, I tried to sort and index it with tabix, but its not working!
The sort with the line bellow seems to go fine
(grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz
But then, When I try
tabix -p sorted.gff.gz
It does not work! It says:
[E::get_intv] failed to parse TBX_GENERIC, was wrong -p [type] used? The offending line was: "itr6_2569_ AUGUSTUS CDS 1416 1422 . + 0 ID=itr6_2569_pilon_pilon_pilon_pi.g1.t1.cds;Parent=itr6_2569_pilon_pilon_pilon_pi.g1.t1" Segmentation fault (core dumped)
My gff is a PASA update output:
file: # original
itr6_6049_ AUGUSTUS gene 18202 46612 . - . ID=itr6_6049_pi.g765;Name=itr6_6049_pi.g765.t1
itr6_6049_ AUGUSTUS mRNA 18202 46612 . - . ID=itr6_6049_pi.g765.t1;Parent=itr6_6049_pi.g765;Name=itr6_6049_ pi.g765.t1
itr6_6049_ AUGUSTUS exon 46565 46612 . - . ID=itr6_6049_pi.g765.t1.exon1;Parent=itr6_6049_pi.g765.t1
I would appreciate any help.. This is really annoying me because its seems simples, I know =(
Thank you!
this is a new question , not a reply. Open a new question please
Oh sorry, Pierre! I'll do that!
You should use "tabix -p gff filename.gff.gz" not just "tabix -p filename.gff.gz"