hisat2 | Graph-based alignment | Genomics library
kandi X-RAY | hisat2 Summary
kandi X-RAY | hisat2 Summary
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (whole-genome, transcriptome, and exome sequencing data) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for a graph [1], we designed and implemented a graph FM index (GFM), an original approach and its first implementation to the best of our knowledge. In addition to using one global GFM index that represents general population, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover human population). These small indexes (called local indexes) combined with several alignment strategies enable effective alignment of sequencing reads. This new indexing scheme is called Hierarchical Graph FM index (HGFM). We have developed HISAT2 based on the HISAT [2] and Bowtie 2 [3] implementations. See the [HISAT2 website] for more information.
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QUESTION
I want the stderr of all files within a for-loop. So far only the first one in the for loop was written into summary.txt.
My codes:
...ANSWER
Answered 2022-Mar-06 at 19:08You redirect the file descriptor for all commands within the loop.
QUESTION
I am very new to coding so I'm not really sure how to approach this. I wanted to look at some data that we got and sequence them using Bismark. I already used Trim Galore to pare the reads, now I wanted to get the data into Bismark. However, I'm not exactly sure how to approach this. In the documentation it said that it required Perl to run so I downloaded Perl along with the Bismark zip file from github. I also downloaded the bowtie2 zip file and extracted both the zip files into the same directory. I then opened up the Perl command prompt and set the directory to one with my extracted folders. I put this line in:
...ANSWER
Answered 2021-Nov-11 at 20:03I think Bismark and bowtie2 only supports Linux and macOS natively. If you want to use bismark on Windows you can try install it via a *nix emulation systems like Cygwin, MSYS2, or simply use WSL. I tested this on Windows 11 with WSL with Ubuntu 20.04:
Downloaded bowtie2-2.4.4-linux-x86_64.zip and extracted to
~/bowtie2/bowtie2-2.4.4-linux-x86_64folder.Downloaded Bismark-0.23.1.zip and extracted to
~/bismark/Bismark-0.23.1/Tested installation:
QUESTION
I have extracted a zip file (hisat2-2.2.0-Linux_x86_64.zip from https://cloud.biohpc.swmed.edu/index.php/s/hisat2-220-Linux_x86_64/download) in Ubuntu (by right-clicking the file and choose extract here) and this gives me the following file permissions:
ANSWER
Answered 2021-Aug-18 at 22:47Python's zipfile does not support Unix-style permissions inside Zip files, since they are non standard. You can just call the unzip command via the subprocess module:
QUESTION
As in the title, my Snakefile is giving me a SyntaxError for the expand function in the all rule. I am aware that this is typically caused by whitespace/indentation errors HOWEVER I have confirmed that there are no tabs in the file. I've gone through an deleted every whitespace as well as searched the file with grep. I appreciate any advice.
Error Message:
SyntaxError in line 14 of /PATH/to/Snakefile:
Unexpected keyword expand in rule definition (Snakefile, line 14)
Code:
...ANSWER
Answered 2021-Feb-09 at 05:19This is an error from python as the rule all has two functions separated by a comma. In this case the second expand call is causing the error. You could replace the , with a + to resolve the error like given below.
QUESTION
I am unsuccessful in running this small snakemake program for StringTie; the dry-run gives an error of MissingInputException for the "rule stringt", I am unable to understand the issue here since the same directory structures works fine for a different snakemake program.
I have already generated the bam files using "hisat2" and is located in the directory : "/alternate_splice/bam_out/" which is stored as "bamdir".
The snakemake should be able to locate the input file since the names and location are appropriate, however it throws an error every time.
I did look at the pervious snakemake related questions, however could not solve this issue. If anyone can help me out here, it would be great!
...There are 4 samples: for the wildcards, it takes the list from the directory which has the fastq files
ANSWER
Answered 2020-Apr-02 at 08:14As the input you have a variable called tname which isn't used, and I think it is there by mistake:
QUESTION
I have several genome files with suffix .1.ht2l to .8.ht2l
...ANSWER
Answered 2020-Jan-15 at 16:17I think your confusion comes from the fact that hisat wants a prefix to the index files, not all the list of index files. So instead of -x {input.hisat2_index} (i.e. the list of index files) use something like -x /path/to/{wildcards.prefix}.
In other words, the input hisat2_index=expand(...) should be there only to tell snakemake to start this rule only after these files are ready but you don't use them directly (well, hisat does use them of course but you don't pass them on the command line).
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