yasinkaymaz ✭

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• As I read the error line, it says that quality string length is not equal to sequence length; length(QUAL) != length(SEQ). So, you may wanna have your sam/bam file checked/validated...

  in Calling variants in RNAseq Comment by yasinkaymaz January 2016
• Hi @mmterpstra‌ , @ami is right. I used tophat as a splice aligner not star. I personally think reads that span introns or overlap splice acceptor/donor sites (hot spots in my results) should be realigned more sensitively (blat is a good option). Th…

  in Questions about the RNAseq variant discovery workflow Comment by yasinkaymaz April 2014
• @ami I was talking about SNPiR pipeline when I mentioned known junctions because authors provide a set of junction sequences to be used as alignment targets. To me this is a prior info so you need to know where those junctions are to be able to gene…

  in Questions about the RNAseq variant discovery workflow Comment by yasinkaymaz April 2014
• Hi @ami‌ , thanks for the comment. I have run my samples through your pipeline and got some pretty encouraging results. Only issue got my attention was that splice site regions with in exon boundaries (2-3bp inside right before intron) were hot spot…

  in Questions about the RNAseq variant discovery workflow Comment by yasinkaymaz April 2014
• I was wondering if any of you guys have heard of this approach for calling SNVs. Mapping reads to an index including splice junction sequences. Please check this out and tell me what you think. lilab.stanford.edu/SNPiR/readme

  in Questions about the RNAseq variant discovery workflow Comment by yasinkaymaz April 2014
• Ok, now it makes more sense. You don't trim the reads from the spliced position. You only trim small dangling parts. Thanks for the explanation.

  in Questions about the RNAseq variant discovery workflow Comment by yasinkaymaz April 2014
• @ami If you try to align RNAseq reads using directly bowtie/bwa, you will not get any spliced reads (without using any soft-clipping option etc.). Then, when you visualize the alignment on IGV, you would see many miss-matches especially in intron sp…

  in Questions about the RNAseq variant discovery workflow Comment by yasinkaymaz April 2014
• @Geraldine_VdAuwera‌ What I meant by Ncigar was the reads that are represented with an "N" notation in cigar in their bam/sam files, which basically shows that they are spliced reads (specific to RNAseq). I did not mean the reads with Ns (ambiguous …

  in Questions about the RNAseq variant discovery workflow Comment by yasinkaymaz April 2014
• Hi Geraldine, I am currently running GATK for my RNAseq data set (after running TopHat with bowtie2). It is great that you have integrated a tool that takes care of reads with Ncigar. I used to filter out all spliced reads and run GATK. I was wonder…

  in Questions about the RNAseq variant discovery workflow Comment by yasinkaymaz April 2014