error while running Basic4CSeq
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@sinhashruti-9407
Last seen 5.9 years ago

Hi,

I am trying to run Basic4Cseq, but I am always getting the error

Error in if (tempPlus < 0) { : argument is of length zero
Calls: readsToFragments -> readsToFragments
Execution halted.

Can anyone help to solve the issue?

Thanks

Best Regards,

shruti

 

 

 

 

 

Basic4Cseq • 1.0k views
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Hi Shruti,

Did you solved this problem?

I am having the same one while using Basic4Cseq on my 4Cseq data.

Thanks,

Tal

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@carolin-walter-7897
Last seen 4.4 years ago
Germany

Hi Shruti,

sorry for the delay in response, and sorry for the problem that you encountered.

The "tempPlus < 0" error is usually caused by a mismatch of chromosome annotations, e.g. "1,2,...X,Y" in your reference genome and "chr1, chr2...chrX, chrY" in your virtual fragment library. The function "createVirtualFragmentLibrary" has the option "useOnlyIndex", which is per default set to FALSE, so if your reference includes "chr"s, then you might either want to recreate the virtual fragment library with "useOnlyIndex = TRUE", or add the missing "chr" via R to the virtual fragment library. The format of this library is pretty simple, basically just a tab-separated file that should be easy to manipulate.

If this doesn't work, please ask again (either here or per mail; I'm the package's maintainer); to help me track down the problem I'd also ask you to specify both the type of reference genome (like "mm10" or whatever) and the restriction enzymes that you use - this allows me to create the basic virtual fragment library myself and check it for any strange occurrences.

 

Best wishes, and thanks for trying out the package,

Carolin

 

 

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Hi Carolin,

I am also having this kind of problem. I created virtual fragment library with useOnlyIndex=TRUE and also with useOnlyIndex=FALSE, and it didn't solve the problem. I tried to run also the package's files and I got the same error.

Can you think about possible explanation? 

Thanks,

Tal

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Hi Tal,

sorry for the delay (again), my e-mail notification seems to miss questions/comments when the package name is misspelled (in this case, Basic4CSeq instead of Basic4cseq).

As said before, if everything seems to be fine (1...Y or chr1...chrY everywhere, etc), please feel free to contact me directly via e-mail - I'm the package's maintainer.

Best,

Carolin

 

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Hi Carolin,

After testing with different options, I noticed that the problem occurs due to the chrM label. I use chr[123...XYM] labeling in my bam file and Hsapiens hg19 from the BSGenome package uses the same, as well as additional chr names and contigs etc.

With default options in Basic4Cseq, i.e. useOnlyIndex=FALSE and useAllData=TRUE, it runs successfully, However, if I select useAllData=FALSE, it gives the above error whether the other option is TRUE or FALSE, because it does not recognize the chrM, as in the manual of your package it says it can rezognize chrMT instead:

 

useAllData    
Variable that indicates if all data of a BSgenome package is to be used. If FALSE, chromosome names including a "_" are removed, reducing the set of chromosomes to (1 ... 19, X, Y, MT) for the mouse genome or (1 ... 22, X, Y, MT) for the human genome
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