Running DaPars with sample files without leading "chr" and Ensembl gene model

[Farica Zhuang]

Hi,

When running DaPars with Ensembl gene model which has no "chr" prefix and sample files with no leading "chr" to match, I found that I obtain an empty output file. I then looked into the code https://github.com/ZhengXia/dapars/blob/master/src/DaPars_main.py and saw that on line 495, the if condition requires that each line in the sample files to start with "chr" when it says "if....line[0:3] == 'chr'".

Is it true that the model requires leading "chr" in the input files? And if so, is it safe to add leading "chr" for the input sample files and Ensemble gene model file?

Farica

[Shen Tian]

Hi Farica,

Yes you can add chr in your input file. I added and it worked.

Hope it helps.

Shen

Sent from my iPhone

On 28 Aug 2021, at 07:15, Farica Zhuang <far...@seas.upenn.edu> wrote:

Hi,

When running DaPars with Ensembl gene model which has no "chr" prefix and sample files with no leading "chr" to match, I found that I obtain an empty output file. I then looked into the code https://github.com/ZhengXia/dapars/blob/master/src/DaPars_main.py and saw that on line 495, the if condition requires that each line in the sample files to start with "chr" when it says "if....line[0:3] == 'chr'".

Is it true that the model requires leading "chr" in the input files? And if so, is it safe to add leading "chr" for the input sample files and Ensemble gene model file?

Farica

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[Farica Zhuang]

Hi Shen,

Thanks for the reply! I tried adding leading chr in my input files too and it worked as you said, thank you! But do you happen to know if it's safe to simply add the "chr"? I'm wondering because some chromosomes are different, e.g. I read that chrM in hg19 is named MT in GRCh37, so making it chrMT doesn't make it equal to chrM in the hg19 file. My guess is it doesn't matter but just wanted to make sure.

Farica

[Shen Tian]

Hey Farica,

Sorry I’m working with a genome of a non-model organism that I annotated myself, so I’m not quite familiar with human genome.

But I guess it won’t be a problem to match the two systems if you get rid of the three letters later when u finish your analysis? 

Thanks,

Shen

Sent from my iPhone

On 28 Aug 2021, at 12:04, Farica Zhuang <far...@seas.upenn.edu> wrote:



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[Farica Zhuang]

Yes good idea, thank you!