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Hi, I'm wondering does GATK support or plan to support calling variance betwenn two bam files, for example, compare one RNAseq data with pared DNAseq data to identify RNAediting events? Ideally would also support biological replicates. Thanks for …
Thanks, the line may like this: 16 70287177 rs4081753 A G 4734.77 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=0.698;ClippingRankSum=0.168;DB;DP=148;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=1.347;QD=31.99;ReadPosRankSum=-1.467;ANN…
I tried exactly as described in this tutorial. The result I got have some some like this: RefReadCount AltReadCount 1 88 This kind of SNPs usually present in dbsnps. Actually, this is not so uncommon in the result. I t…
@byb121 , I'm also trying to identify RNA-editing sites by RNAseq data only. By the way, the nature method paper used UC instead of HC.
Hi, I'm working with Cancer RNAseq data aiming for finding RNA editing sites. I worked through this pipeline. As discussed in this forum, it seams no tool is good at calling variance (DNA, RNA difference in my case) from cancer RNAseq sample. My q…