Error occured in matchAnnot.py

[lingling huang]

Hi there,
A ERROR occurred during running matchAnnot.py by using human genome hg38 and annotation file v.25. The error message said "chromosome 10 not in annotation" but it actually exist in gtf file. However, there is no such a problem when apply genome hg19 and GTF file v.19. I googled it, someone came across the same one but no perfect answer to solve it. Any help would be appreciated!

[gconcepcion]

Hi there,
A ERROR occurred during running matchAnnot.py by using human genome hg38 and annotation file v.25. The error message said "chromosome 10 not in annotation" but it actually exist in gtf file. However, there is no such a problem when apply genome hg19 and GTF file v.19. I googled it, someone came across the same one but no perfect answer to solve it. Any help would be appreciated!
[ATTACH]4493[/ATTACH]

This is really a question for the author of the software, MatchAnnot, Tom Skelly.

https://github.com/TomSkelly/MatchAnnot

Without seeing your annotations dataset, all I can say is make sure the chromosome names match identically. e.g. (upper case vs lower case characters)

[lingling huang]

This is really a question for the author of the software, MatchAnnot, Tom Skelly.

https://github.com/TomSkelly/MatchAnnot

Without seeing your annotations dataset, all I can say is make sure the chromosome names match identically. e.g. (upper case vs lower case characters)

I have attached screenshot message. Why the result are totally different by using samtools sort and just sort.





I look the name of chromosome by using basic Unix commands such as:

> cut -f1 gencode.v25.chr_patch_hapl_scaff.annotation.gtf | grep -v '^#' | sort | uniq | less
chr1
chr10
chr11
chr12
chr13
chr14
chr15
chr16
:
:

etc.

See, chr10 is actually exist. if the name must be chromosome not chr ,I think the error should first be "chromosome 1 not in annotation ".

[gconcepcion]

I have attached screenshot message. Why the result are totally different by using samtools sort and just sort.
[ATTACH]4494[/ATTACH]

[ATTACH]4495[/ATTACH]

[ATTACH]4496[/ATTACH]
I look the name of chromosome by using basic Unix commands such as:

> cut -f1 gencode.v25.chr_patch_hapl_scaff.annotation.gtf | grep -v '^#' | sort | uniq | less
chr1
chr10
chr11
chr12
chr13
chr14
chr15
chr16
:
:

etc.

See, chr10 is actually exist. if the name must be chromosome not chr ,I think the error should first be "chromosome 1 not in annotation ".

Again, MatchAnnot was written by a third party developer, your question would be better addressed to the author of the software as an issue in the github page I linked in my first post.

This question has already been asked there in the past:

https://github.com/TomSkelly/MatchAnnot/issues/6

[lingling huang]

Again, MatchAnnot was written by a third party developer, your question would be better addressed to the author of the software as an issue in the github page I linked in my first post.

This question has already been asked there in the past:
https://github.com/TomSkelly/MatchAnnot/issues/6

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