User: hylicase

gravatar for hylicase
hylicase20
Reputation:
20
Status:
New User
Location:
New England
Last seen:
3 months, 1 week ago
Joined:
3 years, 7 months ago
Email:
b******@fastmail.com

ngs scientist, wannabe bioinformatician/programmer

Posts by hylicase

<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 23 months ago by hylicase20
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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 23 months ago by hylicase20
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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 23 months ago by hylicase20
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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 23 months ago by hylicase20
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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 23 months ago by hylicase20 • updated 23 months ago by cpad011214k

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