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Questions - samtools

My merge overlapping coordinate python script cost too much memory

I'm trying to choose unique regions for my Non-invasive Prenatal Testing (NIPT) project. I have done following steps: Create an artificial fasta file contains 50bp sequence. On each chromosome, the n...
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Rotomegax

python

samtools

Votes: 0

Answers: 1

Latest Answer

Hopefully this does the trick. Hard to know since I'm working without having the input file or knowing what the output should look like and can't really run the code to check for errors, but here's wh...
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ramzeek

indexing sorted alignment file with samtools index gives "Exec format error"

I am struggling with samtools index. I already did the alignment using "bwa mem reference.fa seq.fastq > alg.sam". The resulting sam file was converted to bam format using "samtools ...
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cicci

sorting

indexing

alignment

samtools

Votes: 0

Answers: 1

Latest Answer

I finally found the mistake. We need to write "samtools sort alg.bam -o sorted.bam" The output can then be used as input for samtools index
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cicci

text encoding not readable on linux

I have a text file which has been previously readable in linux, then I modified some names in it manually on windows and now when I am running it on linux (using samtools), it cannot find exactly thos...
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xyz0o

encode

samtools

Votes: 0

Answers: 0

How to name hundreds of files in increasing order in bash?

I need to download 300 files on the cloud, and name them one by one in increasing order. I can achieve one time by running the following code. The pathname before '>' is the location of the initial...
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Fawkes Liu

bash

shell

bioinformatics

samtools

Votes: 0

Answers: 2

Latest Answer

for ((i=1;i<=300;i++)) do /Applications/samtools-1.14/samtools depth -r nda /Volumes/lab/plants/aligned_data/S${i}_dedup.bam > /Volumes/lab/students/test${i}.txt done
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