I am updating several scripts that were originally made for using the 3.0.1
version of NGSEP. There is a tag used in the script for the FindVarients
command that I haven't been able to identify, -ignoreSX. I was wondering
what its function is and if there is an equivalent function in later
versions?
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Anonymous
Anonymous
-
2021-09-06
Hi,
I am updating several scripts that were originally made for using the 3.0.1 version of NGSEP. There is a tag used in the script for the FindVarients command that I haven't been able to identify, -ignoreSX. I was wondering what its function is and if there is an equivalent function in later versions?
Claire
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Thanks for your interest in NGSEP. The option "-ignoreXS" existed in earlier versions of the software because we used the optional tag "XS" as a quick way to distinguish unique from non-unique bowtie2 alignments. In later versions we replaced this behavior by the more standard option -minMQ. With this option, you can set the minimum mapping score to the value of your preference, according to the read aligner that you are using. Our experiments indicate that 20 is a good default for bwa, bowtie2 and for the reads aligner that we implemented for version 4.
Please let me know if you have any further issues updating your scripts.
Jorge
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi,
I am updating several scripts that were originally made for using the 3.0.1
version of NGSEP. There is a tag used in the script for the FindVarients
command that I haven't been able to identify, -ignoreSX. I was wondering
what its function is and if there is an equivalent function in later
versions?
Hi,
I am updating several scripts that were originally made for using the 3.0.1 version of NGSEP. There is a tag used in the script for the FindVarients command that I haven't been able to identify, -ignoreSX. I was wondering what its function is and if there is an equivalent function in later versions?
Claire
Hi Claire
Thanks for your interest in NGSEP. The option "-ignoreXS" existed in earlier versions of the software because we used the optional tag "XS" as a quick way to distinguish unique from non-unique bowtie2 alignments. In later versions we replaced this behavior by the more standard option -minMQ. With this option, you can set the minimum mapping score to the value of your preference, according to the read aligner that you are using. Our experiments indicate that 20 is a good default for bwa, bowtie2 and for the reads aligner that we implemented for version 4.
Please let me know if you have any further issues updating your scripts.
Jorge