Hi everybody,
I have to convert the genebank file of my virus genome to a gtf file for the aligment of my reads with STAR. I tried different tools, which I found by google search, but I doesn't work unfortunately.
I tried to do it with a perl script I found, called genbank2gtf_mRNA.pl from genebank2gtf and I tried a python script, called gb2gtf.py from lpryszcz, but when using the perl script with a custom chromosome file, I get an empty gtf file and when I tried to use the python script, I get the error: "command didn't found".
Can someone maybe recommend a converter tool or platform which I could use?
And; the genebank file contains splice site annotation from genious, does the conversion translate these coordinates?
Any help is greatfully appreciated :)
Edited: data exemple and tools, I struggled with
My gb data looks something like that:
> FEATURES Location/Qualifiers
> repeat_region 552..634
> /vntifkey="34"
> /label=U5
> CDS 5830..8414
> /vntifkey="4"
> /label=TAT
> /note="HIV-1 tat protein"
> splicing_signal 5934..5935
> /vntifkey="38"
> /label=SA4c
> splicing_signal 5952..5953
> /vntifkey="38"
> /label=SA4a
> splicing_signal 5958..5959
> /vntifkey="38"
> /label=SA4b
> CDS 8787..9407
> /vntifkey="4"
> /label=NEF
> /note="HIV-1 nef protein"
> splicing_signal 5775..5776
> /vntifkey="38"
> /label=SA3
> splicing_signal 6045..6046
> /vntifkey="38"
> /label=SD4
> CDS 5969..8643
> /vntifkey="4"
> /label=REV
> /note="HIV-1 rev protein"
> splicing_signal 5974..5975
> /vntifkey="38"
> /label=SA5
> CDS 2085..5096
> /vntifkey="4"
> /label=POL
> /note="HIV-1 pol polyprotein; (NH2-terminus uncertain)"
> CDS 5041..5619
> /vntifkey="4"
> /label=VIF
> /note="HIV-1 vif protein"
> CDS 5559..5849
> /vntifkey="4"
> /label=VPR
> /note="HIV-1 vpr protein"
> repeat_region 9529..9626
> /vntifkey="34"
> /label=R
> /note="HIV-1 R repeat 3' copy"
> CDS 6061..6306
> /vntifkey="4"
> /label=VPU
> /note="HIV-1 vpu protein"
> CDS 6221..8785
> /vntifkey="4"
> /label=ENV
> /note="HIV-1 envelope polyprotein"
> splicing_signal 6602..6603
> /vntifkey="38"
> /label=(SA6)
> splicing_signal 6720..6721
> /vntifkey="38"
> /label=(SD5)
> /note="Mutation von GT in anderen Isolaten zu AT"
> splicing_signal 8367..8368
> /vntifkey="38"
> /label=SA7
> LTR 1..634
> /vntifkey="19"
> /label=5'_LTR
> /note="HIV-1 5' LTR"
> repeat_region 454..551
> /vntifkey="34"
> /label=R
> /note="HIV-1 R repeat 5' copy"
> intron 744..5776
> /vntifkey="15"
> /label=TAT/REV/NEF_I
> /note="HIV-1 tat, rev, nef mRNA intron 1"
> misc_feature 5743..5744
> /vntifkey="21"
> /label=JNCTN_NY5/LAV
> /note="HIV-1 isolate NY5 DNA end/HIV-1 isolate LAV DNA start"
> intron 6045..8368
> /vntifkey="15"
> /label=TAT_II
> /note="HIV-1 tat cds intron 2"
> CDS 790..2292
> /vntifkey="4"
> /label=GAG
> /note="HIV-1 gag polyprotein"
> insertion_seq 1186..1186
> /vntifkey="14"
> /label=p17/p24
> splicing_signal 4963..4964
> /vntifkey="38"
> /label=SD2
> splicing_signal 744..745
> /vntifkey="38"
> /label=SD1
> splicing_signal 4911..4912
> /vntifkey="38"
> /label=SA1
> splicing_signal 5464..5465
> /vntifkey="38"
> /label=SD3
> polyA_signal 9602..9607
> /vntifkey="25"
> /label=POLY_A
> /note="HIV-1 mRNA polyadenlyation signal"
> splicing_signal 5388..5389
> /vntifkey="38"
> /label=SA2
> intron 6045..8368
> /vntifkey="15"
> /label=REV_II
> /note="HIV-1 rev cds intron 2"
> intron 6045..8368
> /vntifkey="15"
> /label=TAT/REV/NEF_II
> /note="HIV-1 tat, rev, nef mRNA intron 2"
> LTR 9076..9709
> /vntifkey="19"
> /label=3'_LTR
> /note="HIV-1 3' LTR"
> misc_feature 5059..5060
> /vntifkey="21"
> /label=SD2b
> splicing_signal 8335..8336
> /vntifkey="38"
> /label=SA7a
> splicing_signal 8440..8441
> /vntifkey="38"
> /label=SA7b
> splicing_signal 4541..4542
> /vntifkey="38"
> /label=SA1a
> splicing_signal 4722..4723
> /vntifkey="38"
> /label=SD1a BASE COUNT 3423 a 1756 c 2364 g 2166 t ORIGIN
> 1 tggaa....
I think you can use GFF file with STAR aligner.
https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf
2.2.3 Annotations in GFF format.
In addition to the aforementioned options, for GFF3 formatted annotations you need to use --sjdbGTFtagExonParentTranscript Parent. In general, for --sjdbGTFfile files STAR only processes lines which have --sjdbGTFfeatureExon (=exon by default) in the 3rd field (column). The exons are assigned to the transcripts using parent-child relationship defined by the --sjdbGTFtagExonParentTranscript (=transcript id by default) GTF/GFF attribute.
If you would like to convert GFF3 to GTF then you can use gffread. Please look at this post for further details: Convertion Of Gff3 To Gtf
Ok since I want to create a fused genome with the viral DNA as a additional chromosome, I will have to convert my human gtf file in gff3 file format
Sry, I meant, that I either have to convert my big GTF file to a GFF3 file or my small GFF3 file (or genebank file) to GTF file, in order to fuse them for the aligment
Unfortunately gffread does'nt work. I get the error:
Warning: invalid GTF record, transcript_id not found:
pNL4-3 Geneious CDS 2085 5096 . + . Name=POL
Warning: invalid GTF record, transcript_id not found:
pNL4-3 Geneious CDS 5041 5619 . + . Name=VIF
Warning: invalid GTF record, transcript_id not found:
pNL4-3 Geneious CDS 5559 5849 . + . Name=VPR
Warning: invalid GTF record, transcript_id not found:
pNL4-3 Geneious CDS 6061 6306 . + . Name=VPU
My Gff3 file looks like this:
##gff-version 3
##source-version geneious 10.1.3
##Type DNA pNL4-3
##DNA pNL4-3
##TGGAA...
##end-DNA
pNL4-3 Geneious region 1 9709 . + 0 Is_circular=true
pNL4-3 Geneious insertion 1186 1186 . + . Name=p17/p24
pNL4-3 Geneious polyA_signal 9602 9607 . + . Name=POLY_A
pNL4-3 Geneious LTR 9076 9709 . + . Name=3'_LTR
pNL4-3 Geneious LTR 1 634 . + . Name=5'_LTR
pNL4-3 Geneious invisible_Parent 8888 15012 . + . Name=GvHzdFvgSWWztDH65o8llFeG9ws.1346934513538.20
pNL4-3 Geneious invisible_Parent 5304 8887 . + . Name=GvHzdFvgSWWztDH65o8llFeG9ws.1346934513382.19
pNL4-3 Geneious misc_feature 5005 5034 . . . Name=Fragment3
pNL4-3 Geneious misc_feature 5743 5744 . + . Name=JNCTN_NY5/LAV
pNL4-3 Geneious repeat_region 454 551 . + . Name=R
pNL4-3 Geneious repeat_region 9529 9626 . + . Name=R
pNL4-3 Geneious repeat_region 552 634 . + . Name=U5
pNL4-3 Geneious intron 744 5776 . + . Name=TAT/REV/NEF_I
pNL4-3 Geneious intron 6045 8368 . + . Name=TAT_II
pNL4-3 Geneious intron 6045 8368 . + . Name=TAT/REV/NEF_II
pNL4-3 Geneious intron 6045 8368 . + . Name=REV_II
pNL4-3 Geneious CDS 2085 5096 . + . Name=POL
pNL4-3 Geneious CDS 5969 8643 . + . Name=REV
pNL4-3 Geneious CDS 5830 8414 . + . Name=TAT
pNL4-3 Geneious CDS 6221 8785 . + . Name=ENV
pNL4-3 Geneious CDS 790 2292 . + . Name=GAG
pNL4-3 Geneious CDS 8787 9407 . + . Name=NEF
pNL4-3 Geneious CDS 5041 5619 . + . Name=VIF
pNL4-3 Geneious CDS 5559 5849 . + . Name=VPR
pNL4-3 Geneious CDS 6061 6306 . + . Name=VPU
pNL4-3 Geneious splicing signal 5059 5060 . + . Name=SD2b
pNL4-3 Geneious splicing signal 4963 4964 . + . Name=SD2
pNL4-3 Geneious splicing signal 5974 5975 . + . Name=SA5
pNL4-3 Geneious splicing signal 6720 6721 . + . Name=(SD5)
pNL4-3 Geneious splicing signal 744 745 . + . Name=SD1
pNL4-3 Geneious splicing signal 6045 6046 . + . Name=SD4
pNL4-3 Geneious splicing signal 5388 5389 . + . Name=SA2
pNL4-3 Geneious splicing signal 8367 8368 . + . Name=SA7
pNL4-3 Geneious splicing signal 5464 5465 . + . Name=SD3
pNL4-3 Geneious splicing signal 5775 5776 . + . Name=SA3
pNL4-3 Geneious splicing signal 5952 5953 . + . Name=SA4a
pNL4-3 Geneious splicing signal 5934 5935 . + . Name=SA4c
I downloaded the precomiled version of gffread called gffread-0.9.12.Linux_x86_64 and executed this command /Apps/gffread-0.9.12.Linux_x86_64/gffread pNL4-3.gff -T -o pNL4-3.gtf
Ok the error was int the last column, where the transcript ID is stated with Name=transcript_name whereas it only worked with another file were the transcript id was stated with ID=transcript_name
However the gffread transformation does not lead to an gtf file with all exons, of corse. That means I'm still searching the internet.
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Hello,
it would be useful if you tell us which tools you've already tested and what was the problem with them. Otherwise you may get the same recommendations here.
fin swimmer
Oh yes, thank you, that makes sense, I will add it in the question.
Did google search and found genbank2gtf. Never tried. you can explore though
Thank you, I forgot to mention in the question, what I failed to use already. I tried using that tool, but I somehow can not execute it.
It is possible to download viral genomes in the GFF format from the GenBank, have you tried that?
PS: an example of the genome of interest would be useful.
Thank you! I know that, however, I need the file to be in GTF format for the mapping. I could download it as GFF3, however, I also struggeld using availible GFF3 to GTF converter..