雖然這篇Samtools index鄉民發文沒有被收入到精華區：在Samtools index這個話題中，我們另外找到其它相關的精選爆讚文章
[爆卦]Samtools index是什麼？優點缺點精華區懶人包
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#1samtools-index(1) manual page
2022年2月21日 — Index a coordinate-sorted BGZIP-compressed SAM, BAM or CRAM file for fast random access. Note for SAM this only works if the file has been ...
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#2samtools [生物資訊實驗室]
samtools import reference_genome.fa.fai alignment.sam alignment.bam. or
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#3[samtools]index命令简介 - CSDN博客
samtools index 命令的功能描述： 为了能够快速访问bam文件，可以为已经基于坐标排序后bam或者cram的文件创建索引，生成以.bai或者.crai为后缀的索引 ...
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#4from .BAM to .BAI using samtools - Biostars
Samtools index only accepts a single input file, so using a shell metacharacter to specify multiple files will not work. I usually use a shell wrapper to ...
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#5samtools Tutorial - Quinlan Lab
samtools “index” ... Indexing a genome sorted BAM file allows one to quickly extract alignments overlapping particular genomic regions. Moreover, ...
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#6SAMtools - Pasteur.fr
This will create a file named sorted.bam.bai which contains the index. Example: samtools view file.sam >file.bam samtools sort file.bam -o file_sorted.bam.
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#7Running SAMtools Commands - HCC-DOCS
SAMtools Index. The samtools index command creates a new index file that allows fast look-up of the data in a sorted SAM or BAM file.
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#8samtools index - indexes SAM/BAM/CRAM files - Ubuntu ...
samtools index [-bc] [-m INT] aln.sam|aln.bam|aln.cram [out.index]. DESCRIPTION. Index a coordinate-sorted BGZIP-compressed SAM, BAM or CRAM file for fast ...
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#9Dave's Wiki | SAMTools
A BAM index file is usually needed when visualising a BAM file. samtools. samtools index test_sorted.bam test_sorted.bai.
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#10SAMtools - Bioinformatics Notebook - GitHub username - rnnh
Converting a sam alignment file to a sorted, indexed bam file using samtools. Sequence Alignment Map (SAM/ .sam ) is a text-based file is a text-based file ...
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#11samtools使用方法參數整理 - 台部落
samtools 是一個用於操作sam和bam文件的工具合集。 ... 以下兩種命令結果一樣$ samtools index abc.sort.bam $ samtools index abc.sort.bam ...
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#12samtools之index - 组学大讲堂问答社区
samtools 是一个用于操作sam和bam文件的工具合集，包含有许多命令，其中有index用于建立索引，使之快速访问bam文件。
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#13Samtools Index: Chromosome Blocks not Continuous - Stack ...
I keep getting this error trying to run my code for RNA-seq single read data. This was done after using STAR to index the genome and align ...
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#14SAMtools | FSU Research Computing Center
SAMtools. SAM (Sequence Alignment/Map) is a flexible generic format for ... samtools import ex1.fa.fai ex1.sam.gz ex1.bam. Index BAM samtools index ex1.bam.
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#15Samtools index fails on a sorted bam file #1126 - GitHub
I can call the samtools view to convert from SAM to BAM and then sort it with samtools sort . However, when I try to index it the following ...
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#16SAMtools - Wikipedia
These files can then be merged to produce a complete sorted BAM file [TODO - investigate the details of this more carefully]. index: The index command creates a ...
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#17Samtools index for indexing .bam files. - usegalaxy.org support
I would like to use the Samtools index tool. Is that possible for you to install on the Galaxy platform? Thank you for your help in advance.
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#18SAMTOOLS INDEX - Snakemake Wrappers
Index bam file with samtools. URL: Example¶. This wrapper can be used in the following way: rule samtools_index ...
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#19Samtools Index: Chromosome Blocks not Continuous
samtools sort blasted_SRR6649368.bam -o sorted_SRR6649368.bam -n. These error messages indicate that the reads are not sorted by coordinate ...
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#20rna_bowtie.samtools.txt - Animal Genome Databases
Index sorted alignment for fast random access. Index file <aln.bam>.bai will be created. view samtools view [-bhuHS] [-t in.refList] [-o output] [- ...
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#21Tool - Dockstore
site icon Tools · tool icon quay.io/cancercollaboratory/dockstore-tool-samtools-index:1.0 · Contact Author.
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#22samtools index failed - 简书
samtools index failed ... 近来在进行染色体级别基因组的分析。 使用pindel软件对染色体的结构变异进行检测。 在计算过程中发现，和delly不同，pindel需要 ...
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#23[samtools]index命令简介_睿智如水-程序员秘密
samtools index 命令的功能描述： 为了能够快速访问bam文件，可以为已经基于坐标排序后bam或者cram的文件创建索引，生成以.bai或者.crai为后缀的索引文件。
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#24samtools使用大全- IT閱讀
比如samtool的tview命令就需要；gbrowse2顯示reads的比對圖形的時候也需要。IGV顯示比對情況也需要。 Usage: samtools index <in.bam> [out.index]. 例子 ...
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#25samtools 使用简述- 斩毛毛 - 博客园
samtools index file.sort.bam file.sort.bam.bai. 5、faidx. 对fasta文件建立索引，生成.fai文件。可以快速提取fasta文件中的某一序列. samtools ...
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#26xargs -n1 -P5 samtools index - explainshell.com
build and execute command lines from standard input. --max-args=max-args -n max-args Use at most max-args arguments per command line.
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#27How to resolve samtools index error "Chromosome blocks not ...
samtools index mappedPairs.sorted.bam return the following error ... [bam_sort_core] merging from 0 files and 2 in-memory blocks.
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#28samtools - 我們的基因體時代Our "Gene"ration
在position-sorted和indexed過的bam file，我們可以擷取特定區域的alignment狀況使用samtools view這指令。 首先，先將想要使用的bam file用 ...
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#29Re: [Samtools-help] samtools index fails to open the BAM file
bam > > > ly@etsu906119:/Volumes/MyBook/Epi13_38/BAM$ samtools index -b Epi38All.bam > > open: No such file or directory > > [bam_index_build2] fail to open ...
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#30samtools index的一个坑 - 代码先锋网
samtools index 的一个坑，代码先锋网，一个为软件开发程序员提供代码片段和技术文章聚合的网站。
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#31How to index a CRAM file on Terra with samtools?
If I put the CRAM files in my workspace bucket, samtools cannot find it. !samtools index gs://[path to cram].
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#32Manipulating SAM/BAM alignment files - Homer Software and ...
Sometimes they need to be sorted, or have an index, and samtools is an easy way to create one. BEDtools will also be covered at the end to demonstrate some ...
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#33samtools failed to index if sorted by name - SEQanswers
Failed second index. Any chances to get some data? dep, Illumina/Solexa, 6, 04-22-2015 08:23 AM. bam files not sorted by samtools sort ...
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#34BAM | Integrative Genomics Viewer - Broad Institute
SAM files can be sorted and indexed using igvtools. Note: The .SAI index is an IGV format, and it does not work with samtools or any other application.
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#35samtools index - Bioinformatic tools - Truwl
samtools index [-bc] [-m INT] aln.bam|aln.cram [out.index] Index a coordinate-sorted BAM or CRAM file for fast random access. (Note that this does not work ...
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#36Alignment Visualization | Griffith Lab - RNA-seq
Before we can view our alignments in the IGV browser we need to index our BAM files. We will use samtools index for this purpose.
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#37samtools基本命令实例
samtools index test_sorted.bam test_sorted.bai ... samtools flagstat NA06984.chrom16. ... samtools view -h -f 0x0040 test.bam > test_first_pair.sam.
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#38samtools常用命令详解 - 陈连福的生信博客
4.index. 必须对bam文件进行默认情况下的排序后，才能进行index。否则会报错。 建立索引后将产生后缀为 ...
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#39Parallel xargs by Chr - DNAnexus Documentation
The SAMtools compiled binary is placed directory in the <applet dir>/resources directory. ... samtools index "${mappings_bam_name}" || indexsuccess=false.
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#40"samtools index" did not work #27 - githubmemory
Hello, I tried the samtools playground, but seems samtools index did not work. Here is the message: samtools index: failed to create or write index. Thanks.
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#41[samtools] index: BAM 파일 indexing 하기 : 네이버 블로그
Usage: samtools index [-bc] [-m INT] <in.bam> [out.index] Options: -b Generate BAI-format index for BAM files [default] -c Generate ...
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#42BAM Track Format - UCSC Genome Browser
For custom track display, the main advantage of indexed BAM over PSL and other ... samtools sort my.bam my.sorted samtools index my.sorted.bam
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#43使用SAMtools将SAM文件转换为BAM文件、排序、建立索引
index :索引排序比对; faidx: 建立FASTA索引，提取部分序列; tview: 文本格式查看序列; pileup: 产生基于位置的结果和consensus/indel calling.
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#44samtools index 显示bam文件没有完全排序 - BBSMAX
[怪毛匠子整理] samtools学习及使用范例,以及官方文档详解#第一步:把sam文件转换成bam文件,我们得到map.bam文件system"samtools view -bS map.sam > map.bam"; ...
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#45Samtools Introduction Version 0.1.19 General Tips
samtools index aln.sorted.bam samtools idxstats aln.sorted.bam samtools merge out.bam in1.bam in2.bam in3.bam samtools faidx ref.fasta samtools pileup -vcf ...
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#46软件介绍之Samtools - 云+社区- 腾讯云
如下图所示：选择hg19和mm10的index，文章中RNA-S... 文献笔记七十一：REDO根据vcf文件检测植物细胞器基因组RNA编辑位点.
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#47Indexed file formats tutorial · JBrowse 1
We are going to use samtools to create a "FASTA index" using their faidx command. FASTA indexing allows even very large FASTA files to be downloaded into ...
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#48samtools on Biowulf - NIH HPC
However, they are in fact made up of a number of compressed blocks which facilitates indexing and random access. tabix is used to index bgzip ...
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#49SAMtools - Sheffield HPC Documentation
SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per- ...
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#50samtools(1) - Linux man page
samtools index aln.sorted.bam ... bcftools index in.bcf ... Samtools is also able to open a BAM (not SAM) file on a remote FTP or HTTP server if the BAM ...
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#51bam 파일 인덱싱
검색해 보니 먼저 bam파일을 sorting을 한 후 indexing 을 해야하는 것 같다. samtools sort bamfile.bam. samtools index bamfile.bam. 를 실행한다.
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#52[samtools]index命令简介_睿智如水-程序员ITS404_bam index
samtools index 命令的功能描述： 为了能够快速访问bam文件，可以为已经基于坐标排序后bam或者cram的文件创建索引，生成以.bai或者.crai为后缀的索引文件。
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#53操作SAM文件,就用Samtools工具集 - 知乎专栏
samtools index sample.sort.bam. 生成索引，产生.bai文件，用于快速检索reads，必须进行排序后再index。tview前就需要index.
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#54samtools
samtools は、sam（Sequence Alignment/Map）ファイルとbam（Binary ... samtools view -@ 8 -Sb file.sam > file.bam ... samtools index file_sorted.bam.
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#55samtools使用方法總結 - 雪花台湾
Usage: samtools index <in.bam> [out.index]. 例子：. 以下兩種命令結果一樣 ... -f FILE The faidx-indexed reference file in the FASTA format.
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#56【6.2】samtools - Sam' Note
2.3 sort，index. 用samtools排序和然后建立索引. samtools sort eg2.bam eg2.sorted samtools index eg2.sorted.bam.
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#57SAMtools - Cell Innovation
BAMファイルを染色体,座標順で並び替えし、index付加できるようにする。 BAMに対するindex付加の前処理。 3, mpileup, pileup(ゲノム ...
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#58批量samtools index *.bam file_自由如风 - 博客- 新浪
$ for i in *tophat/accepted_hits.bam;do echo $i;samtools index $i; done;. the command above creates a searchable index for each map file so that ...
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#59Rsamtools: Binary alignment (BAM), FASTA, variant call (BCF ...
Index. 64. Rsamtools-package. 'samtools' aligned sequence utilities interface. Description. This package provides facilities for parsing samtools BAM ...
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#60scanBam: Import, count, index, filter, sort, and merge 'BAM ...
indexBam creates an index for each BAM file specified, analogous to the 'samtools index' function. mergeBam merges 2 or more sorted BAM files. As with samtools, ...
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#61Parsing and analyzing BAM files - Data science blog
... .bai file) # indexing allows fast random access of records of sorted BAM files samtools index -@ 16 PC14_L001_R1_pos_sorted.bam.
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#62SAMtools - an overview | ScienceDirect Topics
$samtools index hsa-nsc-vs-chr-sorted.bam. These sorted BAM files, along with the alignment results of the sRNA profiles to the genome in SAM or BAM format ...
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#63SAMtools - 인코덤, 생물정보 전문위키
따라서, 파일 용량을 줄이기 위해서는 binary 형태인 BAM 포맷으로 변환하여 저장한다. SAM은 다양한 얼라인먼트 정보를 저장하고 있으며, index 파일을 ...
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#64Samtools常用命令的总结
Samtools 常用命令的总结 · flags. 1 0x1 这序列是PE双端测序 · view samtools view [options] in.sam|in.bam|in.cram [region...] · index · sort · merge
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#65samtools index的一个坑_u014210048的专栏-程序员ITS203
今天被自己坑了一把。samtools index a.bam b.bam上面这样写，b.bam将是a.bam的bai文件。如果写作samtools index a.bam则会生成一个a.bam.bai文件，这个a.bam.bai文件 ...
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#66SAMtools - Docs CSC
SAMtools provides tools for using and manipulating SAM and BAM formatted alignments. You can use SAMtools for example for indexing, variant calling and ...
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#67008-处理SAM、BAM你需要Samtools
作用：直观显示reads比对到基因组的情况，与IGV类似需要先sort和index. samtools tview SRR3589956.sorted.bam hg19.fasta.
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#68使用BWA、GATK、Samtools软件进行基因测序 - 阿里云帮助文档
samtools index ERR250971.markdup.bam. 重新校正碱基质量值。 利用已有的snp及indels数据库，建立相关模型，构建重校准表。
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#69对sam/bam文件进行操作 - 代码交流
如果想对sam文件建立索引，那么可以使用tabix命令创建。 Usage: samtools index [-bc] [-m INT] aln.bam |aln.cram [out.index] Options: -b ...
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#70Wiki: Bioinformatics | 10 - Oliver Elliott
10. Samtools. As we remarked above, sam format is a common file structure in which to store aligned sequence data. ... samtools index myfile.sorted.bam
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#71Sequence Alignment/Map format and SAMtools | Bioinformatics
SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus ...
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#72Filtering with SAMTools - Core NGS Tools - UT Austin Wikis
Index BAM files that have been sorted (samtools index); Filter alignment records based on BAM flags, mapping quality or location (samtools view).
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#73SAMtools: get breadth of coverage - Metagenomics.wiki
create samtools index. samtools index mapping_result_sorted.bam. # get total number of bases covered at MIN_COVERAGE_DEPTH or higher.
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#74Sequences and Genomic Features 7: SAMtools I - Week Two
Bioinformatics, Samtools, Unix, Command-Line Interface ... SAMtools index, and that's very simple, so we just have to specify the index file ...
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#75SOPs/miningSAMBAM – BaRC Wiki
(Use 'samtools view -h reads.bam' to print the header with the mapped reads.) Many operations (such as sorting and indexing) work only on BAM files. For ...
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#76Sambamba vs Samtools - Genome Spot
Lets try 1-thread SAM-to-BAM conversion and sorting with Samtools. $ time samtools view -Shb ... time samtools index Sequence_samtools.bam
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#77An alternative exome sequencing pipeline using bowtie2 and ...
If you do step 3 with the index found at the above link, which includes random contigs, but then you try to run samtools with an hg19.fa that ...
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#78samtools | 生信菜鸟团
samtools index ${i%.*}.sorted.bam. samtools mpileup -f /home/jmzeng/ref-database/hg19.fa ${i%.*}.sorted.bam >${i%.*}.mpileup. samtools mpileup -guSDf ...
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#79samtools in parallel - Recipes, scripts and genomics
Consider a case where you have multiple SAM files in a folder and they need to be converted to BAM and indexed. here is a slow way to achive it ...
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#80Bug #53705 for Bio-SamTools: $index undefined prior ... - CPAN
Subject: $index undefined prior to coverage call. Date: Fri, 15 Jan 2010 09:01:53 +1030. To: [email protected].
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#81Bioinformatics Core
Since bedtools requires sorted and indexed files to be able to find gene counts. $ module load samtools/0.0.19 $ samtools view -bT index/mm10.fa ...
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#82samtools index not bgzf compressed - Mobilefactbd.com
Samtools does not retrieve the entire alignment file unless it is asked to do so. To achieve this, the BAM file index uses virtual file offsets ...
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#83samtools工具的使用-测序原理-数据格式 - 生信技能树
1）samtools简介-背景：前面我们讲过sam/bam格式，sam文件虽然是可读的文本文件形式， ... 2.2.4）samtools index RNA-seq.bam #对比对文件建立索引
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#84[samtools]index命令简介 - 极客分享
samtools index 命令的功能描述： 为了能够快速访问bam文件，可以为已经基于坐标排序后bam或者cram的文件创建索引，生成以.bai或者.crai为后缀的索引 ...
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#85samtools で sam/bam ファイルを操作する - The Cat Way
sam を bam に変換し index を作成する. シーケンスリードのゲノムマッピングツールであるbowtie2や HISAT2, Tophat もsamファイルを出力する。これをbam ...
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#86Samtools guide: learning how to filter and manipulate with ...
It imports from and exports to the SAM (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows to retrieve reads in any regions swiftly.
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#87samtools升级至1.3 | GeneDock 文档
Usage: samtools <command> [options] Commands: -- Indexing dict create a sequence dictionary file faidx index/extract FASTA index index ...
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#88Samtools - BITS wiki
samtools index cleaned.bam && rm bad.bam tmp.bam # merge multiple BAM files into one sorted file # from http://www.biostars.org/p/9864/
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#89Bioinformatics Data Skills: Reproducible and Robust Research ...
The BAM file must be sorted first, and we cannot index SAM files. To index a position-sorted BAM file, we simply use: $ samtools index celegans_sorted.bam ...
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#90生物人的電腦教室：高通量定序分析一次搞定: 2016年修訂版
建立索引的指令更簡單,就是把主程式的參數改成index,後面加上排序後的BAM檔案路徑即可。承上面的例子,指令為./samtools index ~/result/result.sort.bam。
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#91Cloud Broker and Cloudlet for Workflow Scheduling
Bwa index provides indexing the reference DNA. Bwa aln provides mapping pair between reference-data and sample data. Bwa sampe merges the pair. SAMtools ...
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#92Genomics in the Cloud: Using Docker, GATK, and WDL in Terra
But wait, there's more: ${samtools_path} index -b ${sample_name}.bam This runs "samtools index" on the newly created BAM file, which makes sense.
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#93Bioinformatics: A Practical Handbook Of Next Generation ...
Sort alignment with reference coordinate order samtools sort -T aln.tmp.sort ... Index alignment samtools index aln-pe.bwa_sorted.bam This will produce BAM ...
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#94Computational Non-coding RNA Biology - 第 126 頁 - Google 圖書結果
... Sort, and Index the Alignment Results In the second step, the obtained SAM files were converted to BAM format and were sorted and indexed with SAMTools ...
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#95RNA-seq Data Analysis: A Practical Approach
Indexing enables fast retrieval of alignments, and it is required by ... This command requires that an index file is present. samtools view –b –o ...
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#96Bam To Gvcf bam to gvcf. The records in a GVCF include an ...
Step 4: Merge BAMs and build index. ... then sort and index them (Samtools) Perform variant calling on the sorted BAM files (GATK) Get genotypes in GVCF ...
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#97Bwa Python - LUA Cologne
Review the Alert server for any errors/warnings. bwa index -a bwtsw ... The basic steps are 'samtools faidx' to index the reference genome ...
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#98Gatk4 Cnv gatk4 cnv. After finishing, the GMEF will return the ...
... Developer Docs; Tutorials; Bioconda @ Github; Package Index. ... In GATK4, the term "interval list" also refers to samtools-style genomic coordinate ...
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