User: sarah.kettelkamp

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Posts by sarah.kettelkamp

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Comment: C: Issues with Marking Duplicates in Picard
... So while I was waiting for your response, I tried doing samtools sort -@ 4 -m 30G S1_merged.bam S1_sorted.bam And it worked and only gave me one file! But then I tried doing the MarkDuplicates and it still did the same thing as before. I must be doing something wrong at this step. ...
written 8 months ago by sarah.kettelkamp0
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Comment: C: Issues with Marking Duplicates in Picard
... I tried doing samtools sort -o S1_sorted.bam S1_merged.bam and it told me "fail to open file S1_sorted.bam" ...
written 8 months ago by sarah.kettelkamp0
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Comment: C: Issues with Marking Duplicates in Picard
... Oh dang, okay. Let me trying doing the sort the way you listed. Hopefully that helps. Thanks! ...
written 8 months ago by sarah.kettelkamp0
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Comment: C: Issues with Marking Duplicates in Picard
... ![I linked a screenshot of my terminal showing what it gives me][1] https://imgur.com/pUmF8lh ...
written 8 months ago by sarah.kettelkamp0
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Issues with Marking Duplicates in Picard
... Hi everyone! So I have been tasked with analyzing some sequence data even though I have no clue what I'm doing. I was given some data from 11 samples (S1, S2, etc.), each with a singles file as well as a forward read file (R1) and a reverse read file (R2). In addition, each sample was run in two di ...
gatk picard samtools sorting bwa written 8 months ago by sarah.kettelkamp0 • updated 8 months ago by goodez460

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