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Amer Ghalawinji
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@amer-ghalawinji-14376
Last seen 5.8 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 server.whorke.de processing sample /testread.fasta : bowtie (CtoT) failed to perform the alignments.
Any suggestion?
Thanks in advance!
Best,
Amer
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 (http://bowtie-bio.sourceforge.net/manual.shtml#the--v-alignment-mode) you can read that
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).
Hi Amer
Why do you want to provide "alignment parameters"? Have you read the help text for qAlign?
Regards, Hans-Rudolf