User: brendes

gravatar for brendes
brendes20
Reputation:
20
Status:
New User
Location:
Gloucester, MA
Last seen:
2 months ago
Joined:
3 years, 1 month ago
Email:
b******@fastmail.com

dad, ngs scientist, aspiring bioinformatician

Posts by brendes

<prev • 5 results • page 1 of 1 • next >
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Comment: C: Find bams with identical names and merge them
... Thank you for your response. I found a working solution via the shell, but will explore awk further. ...
written 16 months ago by brendes20
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Comment: C: Find bams with identical names and merge them
... I adapted this to work for my situation: folder1=$1 folder2=$2 # since i expect both folders to have the same filenames, # checking just first folder should be fine find_ds_bams () { find "$folder1"/*/full -type f -name "*.bam" -exec basename {} \; } for i in ...
written 16 months ago by brendes20
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Comment: C: Using flowcell name as file name for FASTQ file
... You can use standard unix tools (such as `cut`, `awk`, `tr`, `grep`, etc) or non-standard ones (e.g.,`bioawk`) to extract metadata from your fastqs. Like genomax said, you'd need to extract some other identifier(s) in order to make your filenames unique. ...
written 16 months ago by brendes20
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Comment: C: Find bams with identical names and merge them
... Definitely not my intention to have people write it for me. I updated the post with what I've got. Thanks for following up. ...
written 16 months ago by brendes20
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Find bams with identical names and merge them
... I'm trying to merge different bam files with the same name (and, theoretically, the same sequence). They are the same set of libraries sequenced at two different times, and I want to merge the matching pairs in order to simulate greater sequencing depth. I can do this just fine with two bams using ...
shell picard samtools sam bam written 16 months ago by brendes20 • updated 16 months ago by cpad011213k

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