It works using ucsc genome gft file
1) cufflinks
/home/xusheng/Biosoft/cufflinks-1.0.3.Linux_x86_64/cufflinks -p 16 -g /home/xusheng/GenomeSequence/Human/refGene.gtf -o AD1 AD1_accepted_hits.bam
2) cuffcompare
/home/xusheng/Biosoft/cufflinks-1.0.3.Linux_x86_64/cuffcompare -V -r /home/xusheng/GenomeSequence/Human/refGene.gtf -s /home/xusheng/GenomeSequence/Human/hg19.fa -R -o s7_s8_refGene AD1/transcripts.gtf Nor3/transcripts.gtf
3. cuffdiff
home/xusheng/Biosoft/cufflinks-1.0.3.Linux_x86_64/cuffdiff -p 16 s7_s8_refGene.combined.gtf AD1/AD1_accepted_hits.bam Nor3/Nor3_accepted_hits.bam
Saturday, July 30, 2011
Friday, July 29, 2011
Cufflinks problem
After running tophat, we get accepted_hits.bam file
1. /home/xusheng/Biosoft/cufflinks-1.0.3.Linux_x86_64/cufflinks -p 16 -g /home/xusheng/GenomeSequence/Human/Homo_sapiens.GRCh37.63.gtf Nor3_accepted_hits.bam
/home/xusheng/Biosoft/cufflinks-1.0.3.Linux_x86_64/cufflinks -p 16 -g Genes_July_2010_hg19.gff AD3_accepted_hits.bam (gff file only contain gene info)
remember: 1. use the UCSC gff file or ENSEMBL gff file; 2. specify the sequence file when performing the cuffcompare analysis, as the following command; 3. use -g rather than -G
3. cuffcompare step
/home/xusheng/Biosoft/cufflinks-1.0.3.Linux_x86_64/cuffcompare -o adnor_compare -s /home/xusheng/GenomeSequence/Human/Ensembl/Hs19_Ensembl.fa -r /home/xusheng/GenomeSequence/Human/Homo_sapiens.GRCh37.63.gtf AD1/AD1_transcripts.gtf AD3/AD3_transcripts.gtf AD4/AD4_transcripts.gtf AD6/AD6_transcripts.gtf AD7/AD7_transcripts.gtf Nor3/Nor3_transcripts.gtf Nor4/Nor4_transcripts.gtf Nor5/Nor5_transcripts.gtf Nor7/Nor7_transcripts.gtf
good links:
http://dingo.ucsf.edu/twiki/bin/view/Cores/BioinformaticsCore/RnaSeqAnalysis
tophat-cufflinks-cuffcompare-cuffdiff (2011-03-29 15:28:55)转载
标签： 杂谈 分类： Nextgenerationsequencing
1. Creation of a genome index (needed for Bowtie and TopHat to operate)
bowtie-build genome.fa bowtie_output/genome
2. Alignments of RNA-seq reads to the genome with identification of exon-exon splice functions using TopHat
tophat -o tophat_output/ bowtie_output/genome reads.fastq
3. Assembly of RNA-seq reads into transcripts and report of the RPKM/FPKM using Cufflinks
cufflinks -o cufflinks_output/ --reference-seq genome.fa tophat_output/accepted_hits.bam
4. Comparison of assembled transcripts with a reference annotation, or across experiments, using Cuffcompare
cuffcompare -o cuffcompare_output -r genome.gtf -R cufflinks_output/transcripts.gtf
5. Finding significant changes in transcript expression, splicing, and promoter use using Cuffdiff
cuffdiff -o cuffdiff_output/ cufflinks_output/transcripts.gtf tophat_output/accepted_hits1a.bam,tophat_output/accepted_hits1b.bam tophat_output/accepted_hits2.bam
(in this example, accepted_hits1a.bam and accepted_hits1b.sam are replicates, while accepted_hits2.bam is another experimental condition)
1. /home/xusheng/Biosoft/cufflinks-1.0.3.Linux_x86_64/cufflinks -p 16 -g /home/xusheng/GenomeSequence/Human/Homo_sapiens.GRCh37.63.gtf Nor3_accepted_hits.bam
/home/xusheng/Biosoft/cufflinks-1.0.3.Linux_x86_64/cufflinks -p 16 -g Genes_July_2010_hg19.gff AD3_accepted_hits.bam (gff file only contain gene info)
remember: 1. use the UCSC gff file or ENSEMBL gff file; 2. specify the sequence file when performing the cuffcompare analysis, as the following command; 3. use -g rather than -G
3. cuffcompare step
/home/xusheng/Biosoft/cufflinks-1.0.3.Linux_x86_64/cuffcompare -o adnor_compare -s /home/xusheng/GenomeSequence/Human/Ensembl/Hs19_Ensembl.fa -r /home/xusheng/GenomeSequence/Human/Homo_sapiens.GRCh37.63.gtf AD1/AD1_transcripts.gtf AD3/AD3_transcripts.gtf AD4/AD4_transcripts.gtf AD6/AD6_transcripts.gtf AD7/AD7_transcripts.gtf Nor3/Nor3_transcripts.gtf Nor4/Nor4_transcripts.gtf Nor5/Nor5_transcripts.gtf Nor7/Nor7_transcripts.gtf
good links:
http://dingo.ucsf.edu/twiki/bin/view/Cores/BioinformaticsCore/RnaSeqAnalysis
tophat-cufflinks-cuffcompare-cuffdiff (2011-03-29 15:28:55)转载
标签： 杂谈 分类： Nextgenerationsequencing
1. Creation of a genome index (needed for Bowtie and TopHat to operate)
bowtie-build genome.fa bowtie_output/genome
2. Alignments of RNA-seq reads to the genome with identification of exon-exon splice functions using TopHat
tophat -o tophat_output/ bowtie_output/genome reads.fastq
3. Assembly of RNA-seq reads into transcripts and report of the RPKM/FPKM using Cufflinks
cufflinks -o cufflinks_output/ --reference-seq genome.fa tophat_output/accepted_hits.bam
4. Comparison of assembled transcripts with a reference annotation, or across experiments, using Cuffcompare
cuffcompare -o cuffcompare_output -r genome.gtf -R cufflinks_output/transcripts.gtf
5. Finding significant changes in transcript expression, splicing, and promoter use using Cuffdiff
cuffdiff -o cuffdiff_output/ cufflinks_output/transcripts.gtf tophat_output/accepted_hits1a.bam,tophat_output/accepted_hits1b.bam tophat_output/accepted_hits2.bam
(in this example, accepted_hits1a.bam and accepted_hits1b.sam are replicates, while accepted_hits2.bam is another experimental condition)
Sunday, July 24, 2011
在vi中如何删除^M
在vi中如何删除^M
2011-06-21 12:34:00 发表于互联网事 本文链接: 在vi中如何删除^M
如果你是用某些windows编辑器编辑的文件，很可能就会产生多余的^M转义符合，当然这些符号在wxin下是看不到的。
但是某天，你在linux下，用vim打开，发现文件中很多^M，那是多么的恶心啊，如下图：
这个时候就要vim的替换功能了，替换命令很简单 :%s/^M//g 也就是将全部的^M替换成空。
但是你可能会发现，如果你直接用键盘输入^M，是替换不成功滴，所以这里有个小技巧，^M不是直接输出来的，而是要用 ctrl+v 接下来ctrl+m 才能出现真正的文件中的^M.
上面这行，才是这篇日志记录的主要目的，因为我每次想替代^M总会忘记如何打出^M.
2011-06-21 12:34:00 发表于互联网事 本文链接: 在vi中如何删除^M
如果你是用某些windows编辑器编辑的文件，很可能就会产生多余的^M转义符合，当然这些符号在wxin下是看不到的。
但是某天，你在linux下，用vim打开，发现文件中很多^M，那是多么的恶心啊，如下图：
这个时候就要vim的替换功能了，替换命令很简单 :%s/^M//g 也就是将全部的^M替换成空。
但是你可能会发现，如果你直接用键盘输入^M，是替换不成功滴，所以这里有个小技巧，^M不是直接输出来的，而是要用 ctrl+v 接下来ctrl+m 才能出现真正的文件中的^M.
上面这行，才是这篇日志记录的主要目的，因为我每次想替代^M总会忘记如何打出^M.
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