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KChen-lab / Monopogen

SNV calling from single cell sequencing
GNU General Public License v3.0
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openCRAVAT application #63

Open ariannadib opened 1 month ago

ariannadib commented 1 month ago

Good morning, Thank you very much for the help provided previously. I am trying to use the output derived from the somatic module, i.e. chr.SNV_mat.RDS in the openCRAVAT software but to do so I would need to better understand the data output. In fact, a necessary field in the openCRAVAT input file is: Strand The strand the variant is on. Either '+' (plus strand): Indicates that the genetic variant is located on the positive (or sense) strand or '-' (minus strand): Indicates that the variant is located on the negative (or anti-sense) strand. Is there any way to know this information or maybe since it's RNA I have to act differently?

Any help is appreciated Thank you

jinzhuangdou commented 1 month ago

You can load chr.SNV_mat.RDS using R as dt <- readRDS(file="chr.SNV_mat.RDS"). It is a SNV by cell matrix that is easily understood. Could you try to see whether it works?

ariannadib commented 1 month ago

Possible input files can only be of the vcf, tsv or hgvs format, the information about the strand (- or +) seems to be mandatory. Thank you for your time