User: phylofun

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phylofun10
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Posts by phylofun

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AddOrReplaceReadGroups error -
... I want to do a for loop around the picard tool, AddOrReplaceReadGroups, but I get an error that has something to do with my input and output paths (I think). Can someone tell me where I went wrong with this: # pwd: /Users/phylofun/Downloads/project for i in mapping/*-pe.bam; do ja ...
picard written 4 weeks ago by phylofun10 • updated 4 weeks ago by RamRS20k
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Comment: C: for loop over bwa aln
... There is an error message when I run bwa sampe, but I think the issue begins with bwa aln. No error message occurs when I run bwa aln; however, the .sai output file goes to the current working directory instead of following the path in READ1_list, and the sample name is not written for the .sai file ...
written 4 weeks ago by phylofun10
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6 follow
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for loop over bwa aln
... My for loop around bwa aln and bwa sampe doesn't seem to work. First, I created paths to the read data: ls -1r reads/*/cleaned/*READ1.fastq.gz > READ1_list ls -1r reads/*/cleaned/*READ2.fastq.gz > READ2_list Next, I made a for loop using READ1_list and READ2_list around the bwa al ...
alignment next-gen bwa written 4 weeks ago by phylofun10 • updated 4 weeks ago by jrj.healey10k

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