Error in checkForRemoteErrors(val) : QuasR: can't pass alignment parameters
Entering edit mode
Last seen 5.4 years ago

Hey :)

I am trying to do a bisulfite alignment with qAlign function. This is my command:

align <- qAlign("/analysis/SampleFile.txt","/analysis/refgenome.fa",aligner="Rbowtie",bisulfite="dir",alignmentParameter=" -m 3 -v 5 --best --strata")

I always get the following error whenever i try to pass alignment parameters no matter what the parameters are:

Error in checkForRemoteErrors(val) :
  one node produced an error: Error on processing sample /testread.fasta : bowtie (CtoT) failed to perform the alignments.


Any suggestion?

Thanks in advance!





quasR quasr error alignmentparameters quasr • 1.3k views
Entering edit mode

As Hans-Rudolf already mentioned, changing the QuasR alignment parameters for bisulfite data is not recommended. Regarding the error, what other parameter combinations did you try to conclude that you "always get the following error [...] no matter what the parameters are"? I can reproduce this error on the example data with your provided parameters, but from the bowtie manual ( you can read that

In -v mode, alignments may have no more than V mismatches, where V may be a number from 0 through 3 set using the -v option.

If I set -v to e.g. 2 or 3 rather than 5 (i.e., compliant with the bowtie instructions), I do not get an error (again, of course, even if it "works" it does not mean that it's a recommended thing to do).

Entering edit mode

Hi Amer

Why do you want to provide "alignment parameters"? Have you read the help text for qAlign?

 If ‘alignmentParameter’ is ‘NULL’ (recommended), ‘qAlign’ will
 select default parameters that are suitable for the experiment
 type. Please note that for bisulfite or allele-specific
 experiments, each read is aligned multiple times, and resulting
 alignments need to be combined. This requires special settings for
 the alignment parameters that are not recommended to be changed.

Regards, Hans-Rudolf


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