kandi X-RAY | samtools Summary
kandi X-RAY | samtools Summary
See [INSTALL] INSTALL) for complete details. [Release tarballs][download] contain generated files that have not been committed to this repository, so building the code from a Git repository requires extra steps:. By default, this will build against an HTSlib source tree in ../htslib. You can alter this to a source tree elsewhere or to a previously-installed HTSlib by configuring with --with-htslib=DIR.
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Trending Discussions on samtools
I want to read all files in my current directory and would like to save the result on another directory. The code is below but could not get the files in the excepted directory. Does anyone can help me....
ANSWERAnswered 2022-Mar-24 at 23:55
Here's a fixed version of your code:
I have a BAM file from which I need to extract the two words starting with "PL:Z...", followed by "PR:Z..."
I started trying with the first word, but no luck :...
ANSWERAnswered 2022-Mar-16 at 15:19
You may use this
awk that loops through all the fields and matches a field using regular expression
^P[LR]:Z: and appends it into a variable to print it in the end.
I am new to shell scripting (bash/awk...etc) so please excuse me for my stupid question. I am aware that to many of you this is so easy
I have multiple files that look like this:...
ANSWERAnswered 2022-Mar-19 at 21:53
I suggest with
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 next sequence overlap 40bp from previous sequence
- Align and only chosen no mismatch sequence
I have a .sam file about 40gb, on the next step I try to merge all overlapping coordinates to one .bed file for using in samtools. This is my python script to do that:...
ANSWERAnswered 2022-Mar-14 at 04:13
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 what I've tried to do:
rawand go straight to creating
treat2and go straight to writing to
bedfile. I opened
bedfileright off the bat and everything in your program is done with that file open.
If this does what you need but still crashes, then perhaps you can read through each file twice to get
last_coord at the end of the
treat1 and then read through it again to "recreate" each line of
treat1 individually and apply it to defining what needs to be written into the file.
Without really knowing the details of what you're doing (I do not work anywhere close to a field that would apply samtools).
I have been using the below script however, I keep getting an error on the output. Any ideas why?...
ANSWERAnswered 2022-Feb-25 at 19:45
Suggesting to replace line:
Say one has some process that outputs files (e.g., converting sam to bam files) and one wants the output of the process to be a value channel so that it can be reused many times. Can one do this during the output of the channel? Or, does one have to call an operator (first?) on the queue channel after it has been output and that process completed?
Here is an example:...
ANSWERAnswered 2022-Jan-21 at 03:06
Ultimately this depends on if the 'alignments' channel is already a value channel or not:
A value channel is implicitly created by a process when an input specifies a simple value in the
fromclause. Moreover, a value channel is also implicitly created as output for a process whose inputs are only value channels.
Note that this will create a queue channel:
Hi I am attempting to use bash to iterate through a .txt file which contains the following lines. This is a smaller subset of the full list of fastq files, but all samples follow the same patterns....
ANSWERAnswered 2022-Jan-20 at 14:56
Why not reading 2 lines at a time? Remove
bwa... when you'll be satisfied with the result.
I am new to bash and would like to get help how to run for loop.
Here is my question, I have 10 different sorted bam files(*.sorted.bam) and I would like to do indexing for each sorted bam files.
I know how to run it for single file using the command below...
ANSWERAnswered 2021-Nov-16 at 11:14
you can use the for..in loop like this:
I've essentially created a function which inputs a string, and then adds the integers which appear before each unique letter. (e.g. 21M4D35M, would provide 56M and 4D)....
ANSWERAnswered 2021-Nov-08 at 18:16
An efficient solution would be to used
I have a conda environment where I have packages including bcftools installed. I am using bcftools stats to generate some stats on my VCF files. Then, I want to plot the generated stats using plot-vcfstats, also from bcftools. However, this command turned out to be dependent on certain packages that didn't install when I installed bcftools in my conda env. The output I got when running
ANSWERAnswered 2021-Oct-22 at 04:24
Seems like a mess. Some of the comments in this open issue imply that Conda's
texlive-core is broken, but not really clear there is an authoritative response there.
On osx-64 platform, I can get semi-functionality with the environment:
No vulnerabilities reported
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