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Giulia Corsi

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Latest activity by Giulia Corsi
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    Giulia Corsi commented,

    1. Community
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    3. Error in SplitNCigarReads

    Dear Bhanu,  thank you for taking care of this. I could not identify a subset of the BAM file where the problem is happening, so I have shared one of the problematic BAM files entirely (the smalles...

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    Giulia Corsi commented,

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    3. Error in SplitNCigarReads

    Dear Genevieve, than you for the indications. I re-run picard including the reference genome as follows: picard ValidateSamFile I=SOD1P_A272C_rep2.Dedup.bam MO=1000 R=hg38_primary_refseq.fa The out...

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    Giulia Corsi commented,

    1. Community
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    3. Error in SplitNCigarReads

    Dear Genevieve, thank you for your reply. The only error I see with ValidateSamFile is about the PL argument not being settled, but I get it also for other samples for which I do not have problems ...

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    Giulia Corsi created a post,

    Error in SplitNCigarReads

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    I get the following error with GATK 4.1.8.1 when running SplitNCigarReads after MarkDuplicates on RNA-seq data: java.lang.IllegalArgumentException: contig must be non-null and not equal to *, and s...

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