Hi ,Qing,
I have some problems when I use the GIREMI.
I used STAR+GATK and also samtools to call the SNV, but they all can’t compute the ifRNAE and no significant pvalue_mi.
I don’t understand homozygous SNV in issues 20. attached is the SNV list.
the reads length is 37bp, single strand, strand specificity. I am not sure if the reads length will influence the results. but our sequence depth is very high.
Hi ,Qing, I have some problems when I use the GIREMI. I used STAR+GATK and also samtools to call the SNV, but they all can’t compute the ifRNAE and no significant pvalue_mi.
I don’t understand homozygous SNV in issues 20. attached is the SNV list.
the reads length is 37bp, single strand, strand specificity. I am not sure if the reads length will influence the results. but our sequence depth is very high.
./giremi \ -f hg38.fa \ -l SNV.uniq.data \ -o SNV.out \ -m 5 \ -p 0 \ -s 0 \
I am looking forward to your reply.
Best
Lei results.out.zip SNV.uniq.data.zip