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Forum: Bioinformatics 04-02-2019, 12:38 AM
Replies: 1
Views: 520
Posted By deKoch13
Bash Error "Unexpected token near done"

Hi!

I wrote the following little bash script:

echo Processing...

inputDir="/home/j490h/localhome/fastq/"
output_folder="/home/j490h/localhome/fastq/textfiles/"

for input_FASTQfile in `ls...
Forum: Bioinformatics 03-25-2019, 02:40 AM
Replies: 8
Views: 1,366
Posted By deKoch13
Works now!

Hi Meyana,

it works now!
But you were absolutely right generating a set list and use the fromList function.
I was not aware that fromList creates a binary data frame that is compatible with the...
Forum: Bioinformatics 03-22-2019, 01:31 AM
Replies: 8
Views: 1,366
Posted By deKoch13
This is what I've done: #imported ...

This is what I've done:

#imported
library(UpSetR)

#make input
list.Input = list(set1 = "trimmed_bismark_bt2_pe.bam_mapped_reads.txt",
set2 =...
Forum: Bioinformatics 03-22-2019, 01:05 AM
Replies: 8
Views: 1,366
Posted By deKoch13
Tried it out, but...

Thank you, Meyana.

I tried your idea, but it still won't work.
How do your input data look like?

I just input 3 text files that each contain one column (read identifier from BAM files).
The...
Forum: Bioinformatics 03-21-2019, 07:39 AM
Replies: 8
Views: 1,366
Posted By deKoch13
UpSet R plot, input data format wrong?

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...
Forum: General 03-18-2019, 07:52 AM
Replies: 0
Views: 1,064
Posted By deKoch13
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]
Forum: Bioinformatics 03-14-2019, 05:35 AM
Replies: 1
Views: 826
Posted By deKoch13
Open and read files in 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,...
Forum: General 03-12-2019, 03:03 AM
Replies: 0
Views: 1,043
Posted By deKoch13
Read in script

Hi all,

I want to write a bash script that reads in a 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...
Forum: General 03-11-2019, 06:28 AM
Replies: 5
Views: 1,126
Posted By deKoch13
I looked the "comm" command up. Sounds promising,...

I looked the "comm" command up. Sounds promising, but I am not sure if this works for such big data files with > 1 Million reads. Do you have an idea for a smart python-based solution?
...
Forum: General 03-11-2019, 06:22 AM
Replies: 5
Views: 1,126
Posted By deKoch13
progress

Thank you for the answer!

I already extracted the read names from all files separately using:

> samtools sort -n bam_filename | samtools view | awk -F "\t" '{print $1}' > output_filename
...
Forum: General 03-11-2019, 01:19 AM
Replies: 5
Views: 1,126
Posted By deKoch13
more details

Maybe I should add some information:
We took one sample and generated the BAM files using three different pipelines.
At the moment, we are only interested in the read names (first column of the BAM...
Forum: General 03-11-2019, 12:53 AM
Replies: 5
Views: 1,126
Posted By deKoch13
Working with BAM files

Hi everybody!

This is my first thread in this forum.
Recently, I started an internship in a bioinformatics research group. Unfortunately, I have only little experience regarding programming,...
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