User: Jonas.Koch

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Jonas.Koch0
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Posts by Jonas.Koch

<prev • 4 results • page 1 of 1 • next >
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UpSet: Error in start_col:end_col : argument of length 0
... Hi! I processed 3 BAM files that were generated from 3 different pipelines, so in total 9 BAM files by writing scripts in bash and python. I extracted the mapped reads from the BAM files and stored them in python sets. Then, I performed pair-wise intersection operations to see which reads are commo ...
R upsetr written 5 months ago by Jonas.Koch0 • updated 5 months ago by zx87548.0k
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(Closed) Rename files that are stored in a list in python
... Hi! I generated a list that contains 3 text files list = [path/A.txt, path/B.txt, path/C.txt] Now, I want to remove the paths of the filenames, so that I have: list = [A.txt, B.txt, C.txt] I tried to use the os.path.basename() function in a for loop: for file in list: file = os.path.basename(f ...
python textfiles path basename lists written 5 months ago by Jonas.Koch0
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File handling python
... Hi! I extracted mapped and unmapped reads of different BAM files using a bash script. Now, I want to compare which reads are in which BAM files in python. I imagined to use python sets (union, intersection) to do that. Unfortunately, I have only little python experience. I already could write a sc ...
python file handling written 5 months ago by Jonas.Koch0 • updated 5 months ago by finswimmer12k
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Read In Function for BAM file processing
... Hi all, I want to write a bash script that reads in a BAM file and performs several processing steps with that input file. Can you recommend some ideas to write such a script? I am a beginner and would be very happy for some input. We want to extract mapped and unmapped reads of the BAM files. I h ...
bam script written 5 months ago by Jonas.Koch0

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