User: brendes

gravatar for brendes
brendes20
Reputation:
20
Status:
New User
Location:
Gloucester, MA
Last seen:
15 hours ago
Joined:
1 year, 11 months ago
Email:
b******@fastmail.com

dad, ngs scientist, aspiring bioinformatician

Posts by brendes

<prev • 5 results • page 1 of 1 • next >
0
votes
3
answers
244
views
3
answers
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 11 weeks ago by brendes20
1
vote
3
answers
244
views
3
answers
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 11 weeks ago by brendes20
0
votes
1
answer
227
views
1
answers
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 11 weeks ago by brendes20
0
votes
3
answers
244
views
3
answers
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 11 weeks ago by brendes20
8
votes
3
answers
244
views
6 follow
3
answers
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 11 weeks ago by brendes20 • updated 11 weeks ago by cpad011211k

Latest awards to brendes

Autobiographer 23 months ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 876 users visited in the last hour