Sinem Selvi
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Activity overview
Latest activity by Sinem Selvi-
Sinem Selvi commented,
Hello James Emery It might be rounding as it is small number of bases. But when we work on single genes, total coverage is considered in detail. I created the gene list from refseq as explained in ...
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Sinem Selvi commented,
Hello James Emery thank you for your answer. You can see sample_gene_summary result below. Gene total_coverage average_coverage S19_total_cvg S19_mean_cvg S19_granular_Q1 S19_gran...
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Sinem Selvi commented,
Hello,Thank you to consider the issue. The coverage covers the exon. You can find the interval list below. The gap occurred in the first exon of the interval list (chr15:48936802-48936966). chr15...
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Sinem Selvi commented,
Thank you!
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Sinem Selvi commented,
Hi Megan, Thank you to inform me. I think I should run the pipeline twice with another reference which is Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta . Is it right? Also for both pipel...
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Sinem Selvi commented,
Hello,Thank you to explain the pipeline to me! I successfully obtained the vcf file. I want to be sure everything is correct. The log of the pipeline is below. Running: java -Dsamjdk.use_async_...
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Sinem Selvi commented,
Hello,Thank you for helping. I'm working on a patient bam file and the pipeline starts with it. I understood that I needed a reference bam file in MergeAlignmentBam part out of my original patient ...
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Sinem Selvi commented,
Hello,Firstly, I got the aligned bam file from here: gs://fc-ccb0e231-7c8d-4a45-82a3-0f3584a216c0/40c2c7c9-3d17-40b0-96e6-4b43d2b56250/MitochondriaPipeline/56b9e8ed-898c-4747-b8e5-992c3afe71fa/call...
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Sinem Selvi commented,
Hello, I sorted both files by queryname and run MergeBamAlignment with --SORT_ORDER queryname. I still get the output bam file. But it is not valid and I cannot use it. 10:00:28.936 INFO Native...
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Sinem Selvi commented,
Hi, I could get bam file by changing sort order command (--SORT_ORDER unsorted). There is still the same error but merged bam file is produced. Log: 17:14:19.159 INFO NativeLibraryLoader - Loading...