Search Results
| Search type | Search syntax |
|---|---|
| Tags | [tag] |
| Exact | "words here" |
| Author |
user:1234 user:me (yours) |
| Score |
score:3 (3+) score:0 (none) |
| Answers |
answers:3 (3+) answers:0 (none) isaccepted:yes hasaccepted:no inquestion:1234 |
| Views | views:250 |
| Code | code:"if (foo != bar)" |
| Sections |
title:apples body:"apples oranges" |
| URL | url:"*.example.com" |
| Saves | in:saves |
| Status |
closed:yes duplicate:no migrated:no wiki:no |
| Types |
is:question is:answer |
| Exclude |
-[tag] -apples |
| For more details on advanced search visit our help page | |
Results tagged with samtools
Search options questions only
not deleted
user 6948
Questions specific to interacting with and post-processing sequence alignments using the SAMtools package. For questions specifically about formats SAM, BAM or CRAM use tags sam or bam,
0
votes
1
answer
254
views
How can I run the latest version of samtools on Slurm?
While everything is perfect on my local machine with the samtools version 1.11, it does not work on slurm. … /1.11 # this is what I tried first
module spider samtools/1.11 # this does not help either... …
1
vote
1
answer
264
views
How can I get unmatched reads for defective genomes analysis using bwa and samtools?
it is required before the analysis)
bwa index sequence.fasta
Then, I have installed samtools
cd ..
wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
tar -vxjf samtools … If I got it right - I need this output file to filter with samtools, am I correct? …
2
votes
4
answers
504
views
How to make work programs from the $PATH?
/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
sudo tar -vxjf samtools-1.9.tar.bz2
cd samtools-1.9
sudo make
I did not get exactly what does that mean: (must be in your $PATH) but I have … '
I have no idea how samtools must be accessed, I tried sudo command with python3 but it did not work. …
1
vote
1
answer
2k
views
How can I extract information from .sam files?
I have 10 .sam files after my bowtie2 alignment on ten single-pair sequences. I would like to build a graph based on that output data, however I don't see any other solution but just writing the align …
0
votes
1
answer
356
views
How to perform bowtie2 analysis with slurm?
Official manual for bowtie2 says I can use samtools for that. However when I run the following script I have an error
line 22: bowtie2: command not found
Below is the script:
#! … /bash
#SBATCH --time=05:00:00
#SBATCH --account=def-myaccount
#SBATCH --mem=200000M
#SBATCH [email protected]
#SBATCH --mail-type=All
module load nixpkgs/16.09 intel/2018.3
module load samtools …
3
votes
1
answer
2k
views
How to extract unmatched reads using bwa and samtools?
This step uses a combination of bwa mem and samtools view with the parameters –bS –f4. … .fastq format (since this is the format used by the software later)
samtools fastq sample.unmapped.sam > unmatched.fastq
I wonder if these steps are correct? …