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Question: Error message from 'scanForHeterozygotes' function in AllelicImbalance package
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gravatar for JK
2.8 years ago by
JK10
United States
JK10 wrote:

I generated BAM files using the STAR RNA-Seq aligner and the work stream described in GATK:

 

https://www.broadinstitute.org/gatk/guide/article?id=3891

 

My R command with the error I am running into with these BAM files:

 

> heterozygotePositions <- scanForHeterozygotes(reads, maxReads=1e+07, verbose=T)

Investigating chromosome chr4

Investigating sample 1 out of 33

Error in new[start[i]:(start[i] + length(toKeep[[i]]) - 1), i] <- charList[[i]][toKeep[[i]]] :

  number of items to replace is not a multiple of replacement length

 

I would appreciate some help with this error.

Thank you,

Joe

ADD COMMENTlink modified 2.5 years ago by Jesper Robert Gadin20 • written 2.8 years ago by JK10
0
gravatar for Jesper Robert Gadin
2.5 years ago by
European Union
Jesper Robert Gadin20 wrote:

Hello,

Sorry to be late with my reply!

This error was solved some months ago, see https://github.com/pappewaio/AllelicImbalance/issues/3

Jesper

ADD COMMENTlink written 2.5 years ago by Jesper Robert Gadin20

Yes, this issue is resolved. Thank you.

ADD REPLYlink written 2.5 years ago by JK10
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