NextGenerationSequencing | Construct a flow to analyze NGS data based on R Perl | Genomics library
kandi X-RAY | NextGenerationSequencing Summary
kandi X-RAY | NextGenerationSequencing Summary
| Code | Description | |---|---| | extractLargeData.pl | To extract paired reads on the basis of the policy. The input is the divided file (due to limitation of the memory) from the aligned SAM one by bowtie programs. | | getLargeData.pl | To count each transcript from all divided files and generate one file containing both transcript and its read count. The counting of input files would be dynamic changed due to the limitation of memory. | | cbnCT.pl | To combine both control and treatment files generated by code, getLargeData.pl, transcript level data would show the read counts of both control and treatment simultaneously. | | preprocess.py | The code combined (1) dividing origin alignmant file from bowtie into several subfiles (it depends on the size of memory) and (2) combining the above extractLargeData.pl, getLargeData.pl and cbnCT.pl with the Linux commands. So this code must be executed on the Linux environment. | | extractGene.pl | To simplify the description of transcript name into the format consisting of ensembl gene name, transcript read count and control read count. | | analysisGene.r | To normalize sets of the control and the treatment, and the output would be several results by analyzing methods, such as fold change, expression difference and probability (respresenting whether the difference is significant in the whole system). The used package for normalization in R was NOISeq. | | gene_deep.r | Due to the incomplete analyses of fold change, expression difference or probability, it was necessary to calculate the trend line, to analyze the item far away from the line and to represent significant changes (differences) between the control and the treatment with normalization. Such analyzing method could be achieved by plotting within the code. | | analysis.r | The similar processing with analysysGene.r was trying to normalize sets of the control and the treatment. But targets were transcripts, not genes. The package used in R was NOISeq. The output would be fold change, expression difference and probability. | | extractGeTreData.py | The code was optional for executing and trying to extract the transcript name, gene name from the transcript label so as to simplify the output generated by analysis.r and to read the data more easily. | | combineTtl.r | The similar processing with gene_deep.r was trying to plot the result (the control and treatment normalization) generated by analysis.r. The purpose of combinettl.r was to analyze the item whose expression difference between the control and the treatment was significant. | | getTranscript.r | Both gene_deep.r and combineTtl.r would each output several potential items on the gene and the transcript level. These potential items of both levels did not mean that they were higher probability on the difference between the control and the treatment. Due to several reasons, it was necessay to extract items which were higher normalization and higher fold change (similar with higher difference). The code was trying to combine outputs from the control and the treatment by intersecting them in order to find items whose were potential hits on transcript and gene levels. | | filterDb.py | Due to the limitation of the memory, the annotated file (.GTF) from GENCODE would be impossible to load the entire file. The code was designed to extract the potential data from the annotated database on the basis of the gene name in getTranscript.r. The process was first to get total gene name from the result generated by getTranscript.r and then executed the pattern matching in annotated file to extract potential entries to a new database. | | annotated.pm | The self-designed package used in Perl environment was constructed by data type of "class" and was implemented by pointer. The package defined the column needed to be stored. And the package would be used in another perl code named getAnnotated.pl. | | getAnnotated.pl | The code used the package, annotated.pm, and was implemented by dynamic allocation memory. The code would output the potential items with their transctipt level, control level and annotated data. The result would be further analyzed by biological experiments. |.
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Trending Discussions on Genomics
QUESTION
I´m working with two text files that look like this: File 1
...ANSWER
Answered 2022-Apr-09 at 00:49Perhaps you are after this?
QUESTION
I'm using the software plink2 (https://www.cog-genomics.org/plink/2.0/) and I'm trying to iterate over 3 variables.
This software admits an input file with .ped extention file and an exclude file with .txt extention which contains a list of names to be excluded from the input file.
The idea is to iterate over the input files and then over exclude files to generate single outputfiles.
- Input files: Highland.ped - Midland.ped - Lowland.ped
- Exclude-map files: HighlandMidland.txt - HighlandLowland.txt - MidlandLowland.txt
- Output files: HighlandMidland - HighlandLowland - MidlandHighland - MidlandLowland - LowlandHighland - LowlandMidland
The general code is:
...ANSWER
Answered 2021-Dec-09 at 23:50Honestly, I think your current code is quite clear; but if you really want to write this as a loop, here's one possibility:
QUESTION
From this example string:
...ANSWER
Answered 2021-Dec-09 at 01:11use regexp_extract(col, r"&q;Stockcode&q;:([^/$]*?),&q;.*")
if applied to sample data in your question - output is
QUESTION
I am making a code which takes in jumble word and returns a unjumbled word , the data.json contains a list and here take a word one-by-one and check if it contains all the characters of the word and later checking if the length is same , but the problem is when i enter a word as helol then the l is checked twice and giving me some other outputs including the main one(hello). i know why does it happen but i cant get a fix to it
...ANSWER
Answered 2021-Nov-25 at 18:33As I understand it you are trying to identify all possible matches for the jumbled string in your list. You could sort the letters in the jumbled word and match the resulting list against sorted lists of the words in your data file.
QUESTION
I am trying to use plink1.9 to split multiallelic into biallelic. The input is that
...ANSWER
Answered 2021-Nov-17 at 09:45I used bcftools to complete the task.
QUESTION
I have a FASTA file that has about 300000 sequences but some of the sequences are like these
...ANSWER
Answered 2021-Oct-12 at 20:28You can match your non-X containing FASTA entries with the regex >.+\n[^X]+\n
. This checks for a substring starting with >
having a first line of anything (the FASTA header), which is followed by characters not containing an X until you reach a line break.
For example:
QUESTION
For example, I have two strings:
...ANSWER
Answered 2021-Oct-04 at 22:27For your example your pattern would be:
QUESTION
I am currently trying to run genomic analyses pipelines using Hail(library for genomics analyses written in python and Scala). Recently, Apache Spark 3 was released and it supported GPU usage.
I tried spark-rapids library start an on-premise slurm cluster with gpu nodes. I was able to initialise the cluster. However, when I tried running hail tasks, the executors keep getting killed.
On querying in Hail forum, I got the response that
That’s a GPU code generator for Spark-SQL, and Hail doesn’t use any Spark-SQL interfaces, only the RDD interfaces.
So, does Spark3 not support GPU usage for RDD interfaces?
...ANSWER
Answered 2021-Sep-23 at 05:53As of now, spark-rapids doesn't support GPU usage for RDD interfaces.
Source: Link
Apache Spark 3.0+ lets users provide a plugin that can replace the backend for SQL and DataFrame operations. This requires no API changes from the user. The plugin will replace SQL operations it supports with GPU accelerated versions. If an operation is not supported it will fall back to using the Spark CPU version. Note that the plugin cannot accelerate operations that manipulate RDDs directly.
Here, an answer from spark-rapids team
Source: Link
We do not support running the RDD API on GPUs at this time. We only support the SQL/Dataframe API, and even then only a subset of the operators. This is because we are translating individual Catalyst operators into GPU enabled equivalent operators. I would love to be able to support the RDD API, but that would require us to be able to take arbitrary java, scala, and python code and run it on the GPU. We are investigating ways to try to accomplish some of this, but right now it is very difficult to do. That is especially true for libraries like Hail, which use python as an API, but the data analysis is done in C/C++.
QUESTION
I have 1500 files with the same format (the .scount file format from PLINK2 https://www.cog-genomics.org/plink/2.0/formats#scount), an example is below:
...ANSWER
Answered 2021-Sep-07 at 11:10a tidyverse
solution
QUESTION
I have been implementing a suite of RecordBatchReaders for a genomics toolset. The standard unit of work is a RecordBatch. I ended up implementing a lot of my own compression and IO tools instead of using the existing utilities in the arrow cpp platform because I was confused about them. Are there any clear examples of using the existing compression and file IO utilities to simply get a file stream that inflates standard zlib data? Also, an object diagram for the cpp platform would be helpful in ramping up.
...ANSWER
Answered 2021-Jun-02 at 18:58Here is an example program that inflates a compressed zlib file and reads it as CSV.
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