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l**********1
发帖数: 5204 | 2 Samtool file
flag inside sam file
SEQanswers - Bioinformatics — I got a read aligned as below: ~ HWI-1KL138:2
:2105:12847:125331#GCCAATGCCAAT 161 chr1 12036 1 74M = 12645 1188
CTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAGTGGGATGGG
hhhhhhhhhhhghhhhhhhhhhhhhhhhhheffffdffffhhhghhehefhhhhhghhfhfffWdbfffbffff
NM:i:0 NH:i:3 CC:Z:chr15 CP:i:102519061 HI:i:0 ~ The flag here is 161=128+32
+1. 128 means 2nd pair; 32 means mated reverse strand; 1 means paired read.
I am wondering why th... 阅读全帖 |
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l**********1
发帖数: 5204 | 3 Try this one
SpliceMap:
//seqanswers.com/wiki/SpliceMap
from
//seqanswers.com/wiki/Software/list |
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l**********1
发帖数: 5204 | 4 plus 各取所需 用C++ or Perl or python or R etc 取决于生信分析的对象
样品数量和目的项目
比如楼主的问题 如是 NGS high.through raw data 也可 try python based
Bcbio-nextgen
cited,
Summary: Python scripts and modules for automated next gen sequencing
analysis. These provide a fully automated pipeline for taking sequencing
results from an Illumina sequencer, converting them to standard Fastq format
, aligning to a reference genome, doing SNP calling, and producing a summary
PDF of results
web link:
HTTP: //seqanswers.com/wik... 阅读全帖 |
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l**********1
发帖数: 5204 | 5 Bedutils
NGSUtils is a suite of software tools for working with next-generation
sequencing datasets. Staring in 2009, we (Liu Lab @ Indiana University
School of Medicine) starting working with next-generation sequencing data.
We initially started doing custom coding for each project in a one-off
manner. It quickly became apparent that this was an inefficient manner to
work, so we started assembling smaller utilities that could be adapted into
larger, more complicated, workflows. We have used the... 阅读全帖 |
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o*********r
发帖数: 446 | 6 应该只需打前一两页和有你名字的那页就行了，highlight任何有帮助的东西，IO才没
时间看全那玩意儿。
你能查到谁在paper里用过你的sequence／anotation数据，claim那个可能更有用。实
在不行，看看seqanswer或者bioconductor是不是有人说过。 |
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n******7
发帖数: 12463 | 7 IT的要求挺合理的，毕竟他们也不是搞这个的，就按照流程走了
不能100%优化配置是不可避免的，实际上你的aligner换个版本/参数就可能对硬件需求
不一样了。你要不是computational的group的话，很多计算都是一次性的，慢个一点其
实无所谓。也就是说，配置的弹性很大，没必要太纠结。alignment把genome index
load进内存就好，没多大
你可以去seqanswers问问做类似工作的都是用什么什么配置，你照葫芦画瓢 |
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l**********1
发帖数: 5204 | 12 try free gsMapper and gsAssembler
cited:
>Installation
Where can I get a copy of the GS-FLX Mapping and Assembly software
I wrote to Roche to ask if we could give copies to people, and they wrote
back to say it is license free for non-commercial usage, so if you need a
copy please go to web link:
//genepool.bio.ed.ac.uk/nextgenbug/faq/roche_454_gs_flx
and
for Bowtie and gsMapper
please refer:
cited
>The 454 reads may be a bit long for Bowtie. You would be better off using
the gsMapper software t... 阅读全帖 |
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l**********1
发帖数: 5204 | 13 你个Bioinformatics PI/PD 就会说Bioinformatics 学士论文 要求很低呀 差很多啊?!
Ps:
NGS ver 1.0 Biostatistics Godfather: Terry Speed:
//www.stat.berkeley.edu/users/terry/Group/software.html
or
//www.stat.berkeley.edu/~terry/
//www.python.org/community/lists/
more tools for NGS 2.0/3.0 version:
//seqanswers.com/forums/showthread.php?t=43 |
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c**********e
发帖数: 70 | 14 Congratulation to him.
-----------------------------
March 14, 2012 | Heng Li, a research scientist at the Broad Institute, is
the winner of the 2012 Benjamin Franklin Award for Open Access in the Life
Sciences.
“I have to say I’m a little surprised,” Li told Bio-IT World, of the
award, though his contributions speak for themselves. Li made essential
contributions to the next generation sequencing (NGS) field with tools like
SAMtools, BWA, MAQ, TreeSoft and TreeFam, many of which began as proj... 阅读全帖 |
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j*p
发帖数: 411 | 16 攒人品，顺便回答一下 iiiir 的问题。
我们尝试过好几种不同的SNP calling的方法，包括GATK, Samtools, Varscan,
SeqGenes, 等，并且做了SNP array 作为gold standard比较各种方法的prediction
power。
从我们的经验，BWA + GATK 最好，sensitivity 和 specificity 都在95%以上。
以下是GATK 的pipeline
假设你有一个control 样品C 和一个样本样品A的pair-end sequencing，共4个文件，C
_R1.fastq, C_R2.fastq, A_R1.fastq and A_R2.fastq如何通过BWA/GATK去找样品A中
的SNPs (相对于C)
假设assembly 用的是hg19，你的BWA index 在这里：/bwa/indexes/hg19
Check this website if you have any questions:
http://seqanswers.com/wiki/How-to/exome_analysis
#s... 阅读全帖 |
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j*p
发帖数: 411 | 17 攒人品，顺便回答一下 iiiir 的问题。
我们尝试过好几种不同的SNP calling的方法，包括GATK, Samtools, Varscan,
SeqGenes, 等，并且做了SNP array 作为gold standard比较各种方法的prediction
power。
从我们的经验，BWA + GATK 最好，sensitivity 和 specificity 都在95%以上。
以下是GATK 的pipeline
假设你有一个control 样品C 和一个样本样品A的pair-end sequencing，共4个文件，C
_R1.fastq, C_R2.fastq, A_R1.fastq and A_R2.fastq如何通过BWA/GATK去找样品A中
的SNPs (相对于C)
假设assembly 用的是hg19，你的BWA index 在这里：/bwa/indexes/hg19
Check this website if you have any questions:
http://seqanswers.com/wiki/How-to/exome_analysis
#s... 阅读全帖 |
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l**********1
发帖数: 5204 | 19 so what? if your found can solve solid wet or hard bio can’t solve non-
linear trend between
count level and variance by Deseq or other softs ?
pls refer,
01-16-2013, 12:40 AM #1
JesperGrud
Junior Member
Location: Odense
Join Date: Aug 2012
Posts: 5
DESeq and independent filtering
Hi everyone
I know this topic has been up a few times, but yet there is a question. So
the basic idea about filtering is that it is done unsupervised to remove
genes that are too lowly expressed to become signif... 阅读全帖 |
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