man Sac
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Activity overview
Latest activity by man Sac-
man Sac commented,
I tried to the next step, nut error was occured. samtools view -b aln.pe.sorted.bam chrM > samtools.chrM.bamgatk RevertSamSpark -I samtools.chrM.bam -O reverted.samtools.chrM.bamjava -jar picard....
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man Sac created a post,
problem regarding mitochondria analysis
REQUIRED for all errors and issues: No read was passed after PrintReads. Hello, I'm currently trying to perform mtDNA analysis. I sequenced 2 amplicons covered the whole mitochondrial genome using ...
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man Sac commented,
Thank you very much. I appreciate the thorough support.
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man Sac commented,
By "local environment," do you mean a local machine like a Mac rather than an HPC? Is it easy to run using Docker on a local machine?
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man Sac commented,
Thank you for your advice. As you mentioned, it seems that Docker is not allowed in my analysis environment. Singularity is available, but as indicated in other questions, this issue is not support...
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man Sac created a post,
error in mitochondria pipeline
Hello. I am currently trying to detect mutations and estimate haplogroups using mitochondrial DNA reads sequenced with MiSeq. I prepared my data like this. bwa index human_ref/resources_broad_hg38_...
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man Sac commented,
Thank you so much for your reply. I will try the pipeline you recommended. Best regards,
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man Sac created a post,
Output in SortSam was not generated
Hello. I am trying to map MiSeq reads to a reference genome and extract mutations using MToolBox, which implements gsnap, GATK, Picard, and other tools. When running the tool with example data, the...