how to make a .tbi file of .gtf.gz?

Question

[KVC_bioinfo]

Hello,

I have a .gtf.gz file which I am going to use in a python code. for using the pysam module in python it requires an indexed file for gtf.gz?

How can I index that file? Thank you in advance.

[Alex Reynolds]

Another option:

$ gunzip -c foo.gtf.gz | gtf2bed - | bgzip -c > foo.bed.gz
$ tabix -p bed foo.bed.gz

[Caizhaoqing]

Yes,you are right ! and you have given a better introduction to this Data Format！

[ATpoint]

Please use ADD REPLY instead of the answer field.

Answer 1

[Caizhaoqing]

I have solved the question!

Firstly you should sort you GTF file (when downloaded, usually it is unsorted.) you may can sort it like:

 (grep ^"#" in.gtf; grep -v ^"#" in.gtf | sort -k1,1 -k4,4n) | bgzip  > in.sorted.gtf.gz

Then you can create your .tbi file of .gtf.gz with commds like this: tabix -p gff human.gtf.gz.

You can try it.

[jixiangj]

you are the best

[finswimmer]

In addition: tabix can be used for indexing and query any tab separated data, that have a column with a name, one with a number and is sorted by this two columns. Use the option -s, -b and optional -e during indexing to define in which columns the name, the beginning and optional the en position is stored.

[fwuffy]

This fails on RefSeq GTFs from NCBI.

You may also need to set the delimiter and sort on end position. I've had better luck with the -V sort (natural version sort) algo on chromosome names, but I think that is a matter of personal preference, whether you want alt contigs interleaved with primary chromosomes, or at the end

(grep ^"#" in.gtf; grep -v ^"#" in.gtf | sort  -t $'\t' -k1,1V -k4,4n -k5,5n) | bgzip  > in.sorted.gtf.gz

Answer 2

[GenoMax]

Using tabix from samtools.

[KVC_bioinfo]

Usage:   tabix <in.tab.bgz> [region1 [region2 [...]]]

Options: -p STR     preset: gff, bed, sam, vcf, psltbl [gff]
         -s INT     sequence name column [1]
         -b INT     start column [4]
         -e INT     end column; can be identical to '-b' [5]
         -S INT     skip first INT lines [0]
         -c CHAR    symbol for comment/meta lines [#]
         -r FILE    replace the header with the content of FILE [null]
         -B         region1 is a BED file (entire file will be read)
         -0         zero-based coordinate
         -h         print also the header lines
         -H         print only the header lines
         -l         list chromosome names
         -f         force to overwrite the index

Yes, that was my first guess. But from this it does not take input of gtf

[GenoMax]

From this page:

Firstly, tabix directly works with a lot of widely used TAB-delimited formats such as GFF/GTF and BED.

[cpad0112]

in addition, gtf =~ gff2

[KVC_bioinfo]

Interesting !

Because their command deos not show it works with gtf:

tabix [-0lf] [-p gff|bed|sam|vcf] [-s seqCol] [-b begCol] [-e endCol] [-S lineSkip] [-c metaChar] in.tab.bgz [region1 [region2 [...]]

I tried using it anyway:

$ tabix -p gtf  human.gtf.gz
[main] unrecognized preset 'gtf'

[Ram]

tabix -p gff human.gtf.gz

formats such as GFF/GTF

probably means the same preset can be used for both GFF and GTF files.

[michi.s]

does not work for me

[Pierre Lindenbaum]

does not work for me

https://meta.stackexchange.com/questions/147616/what-do-you-mean-it-doesnt-work